diff --git a/src/security_scanner/cli/app.py b/src/security_scanner/cli/app.py
index 56132ac..e3e61b4 100644
--- a/src/security_scanner/cli/app.py
+++ b/src/security_scanner/cli/app.py
@@ -13,6 +13,7 @@
 
 from security_scanner.cli.commands import (
     doctor,
+    migrate,
     quickstart,
     report,
     scan,
@@ -21,7 +22,16 @@
     verify,
 )
 
-_COMMAND_MODULES = (scan, report, verify, storage, doctor, quickstart, targets)
+_COMMAND_MODULES = (
+    scan,
+    report,
+    verify,
+    storage,
+    doctor,
+    quickstart,
+    targets,
+    migrate,
+)
 
 
 def build_parser() -> argparse.ArgumentParser:
diff --git a/src/security_scanner/cli/commands/migrate.py b/src/security_scanner/cli/commands/migrate.py
new file mode 100644
index 0000000..c223ad1
--- /dev/null
+++ b/src/security_scanner/cli/commands/migrate.py
@@ -0,0 +1,81 @@
+"""backfill-repo-axis subcommand: migrate legacy REPO# GSI1 rows to shards (#23).
+
+Repo-axis GSI1 rows written before issue #23 live on the unsharded
+``REPO#<repo>`` partition. This command runs the in-place backfill that re-points
+each existing primary item's GSI projection to a ``REPO#<repo>#SHARD#<bucket>``
+partition. It mutates only the GSI key fields of rows that already exist; it never
+copies rows or writes finding payload data.
+
+``--dry-run`` reports the per-entity legacy inventory without mutating anything.
+"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+
+from security_scanner.cli._args import add_storage_args
+from security_scanner.cli._store import dynamodb_config_from_args
+from security_scanner.storage.adapters.nosql_db.repo_axis_migration import (
+    backfill_repo_axis,
+    inventory_legacy_repo_axis,
+)
+from security_scanner.storage.adapters.nosql_db.transport import (
+    make_boto3_resource_and_client,
+)
+
+
+def register(subparsers) -> None:
+    parser = subparsers.add_parser(
+        "backfill-repo-axis",
+        help="Migrate legacy REPO# GSI1 rows to the sharded repo-axis layout (#23).",
+    )
+    add_storage_args(parser, include_jsonl_path="", default_backend="dynamodb")
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Report legacy inventory per entity without mutating anything.",
+    )
+    parser.set_defaults(func=cmd_backfill_repo_axis)
+
+
+def _table_from_args(args: argparse.Namespace):
+    config = dynamodb_config_from_args(args)
+    resource, _client = make_boto3_resource_and_client(config)
+    return resource.Table(config.table_name)
+
+
+def cmd_backfill_repo_axis(args: argparse.Namespace) -> int:
+    """Backfill (or inventory) legacy repo-axis GSI1 rows for the dynamodb store."""
+    if args.storage_backend != "dynamodb":
+        print(
+            "backfill-repo-axis requires --storage-backend dynamodb "
+            f"(got '{args.storage_backend}')",
+            file=sys.stderr,
+        )
+        return 2
+
+    table = _table_from_args(args)
+
+    if args.dry_run:
+        inventory = inventory_legacy_repo_axis(table)
+        print("repo-axis legacy inventory (dry-run, no mutation):")
+        for entity_type, count in inventory.items():
+            print(f"  {entity_type}: {count}")
+        print(f"  total legacy rows: {sum(inventory.values())}")
+        return 0
+
+    report = backfill_repo_axis(table)
+    print("repo-axis backfill report:")
+    for entity_type, counts in report.by_entity.items():
+        print(
+            f"  {entity_type}: inventory={counts.inventory} "
+            f"backfilled={counts.backfilled} skipped={counts.skipped} "
+            f"failed={counts.failed} remaining={counts.remaining}"
+        )
+    any_failed = any(counts.failed for counts in report.by_entity.values())
+    if report.gate_clear and not any_failed:
+        print("gate: CLEAR (no legacy repo-axis rows remain)")
+        return 0
+    print("gate: NOT CLEAR (legacy rows remain or failures occurred)")
+    return 1
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 8219431..9651e85 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -722,4 +722,5 @@ def test_subcommand_registration_order_is_stable():
         "enable-target",
         "disable-target",
         "sync",
+        "backfill-repo-axis",
     ]
diff --git a/tests/test_cli_backfill_repo_axis.py b/tests/test_cli_backfill_repo_axis.py
new file mode 100644
index 0000000..7a97eb7
--- /dev/null
+++ b/tests/test_cli_backfill_repo_axis.py
@@ -0,0 +1,172 @@
+"""Tests for the backfill-repo-axis CLI subcommand (issue #23)."""
+
+from __future__ import annotations
+
+from security_scanner.cli.app import main
+
+
+class _FakeTable:
+    class ConditionalCheckFailedException(Exception):
+        pass
+
+    def __init__(self, items: list[dict]) -> None:
+        self.items = items
+        self.update_calls: list[dict] = []
+
+    def scan(self, **kwargs) -> dict:
+        entity_type = kwargs["ExpressionAttributeValues"][":entity_type"]
+        return {
+            "Items": [dict(i) for i in self.items if i.get("entityType") == entity_type]
+        }
+
+    def update_item(
+        self,
+        *,
+        Key: dict,
+        UpdateExpression: str,
+        ExpressionAttributeValues: dict,
+        ConditionExpression: str | None = None,
+    ) -> dict:
+        self.update_calls.append(Key)
+        item = next(
+            (i for i in self.items if i["PK"] == Key["PK"] and i["SK"] == Key["SK"]),
+            None,
+        )
+        if item is None or (
+            ConditionExpression
+            and "attribute_not_exists(repoAxisVersion)" in ConditionExpression
+            and "repoAxisVersion" in item
+        ):
+            raise self.ConditionalCheckFailedException()
+        for assignment in UpdateExpression.removeprefix("SET ").split(", "):
+            target, value_key = assignment.split(" = ", 1)
+            item[target] = ExpressionAttributeValues[value_key]
+        return {}
+
+
+class _FakeResource:
+    def __init__(self, table: _FakeTable) -> None:
+        self._table = table
+
+    def Table(self, _name: str) -> _FakeTable:  # noqa: N802 - boto3 API shape
+        return self._table
+
+
+def _legacy_finding(repo: str = "fake-org/fake-repo") -> dict:
+    return {
+        "PK": "FINDING#f1",
+        "SK": "META",
+        "entityType": "FINDING",
+        "gsi1pk": f"REPO#{repo}",
+        "gsi1sk": "FINDING#f1",
+        "findingId": "f1",
+        "repo": repo,
+    }
+
+
+def _legacy_ghas(repo: str = "fake-org/fake-repo") -> dict:
+    return {
+        "PK": "GHAS_ALERT#g1",
+        "SK": "META",
+        "entityType": "GHAS_ALERT",
+        "gsi1pk": f"REPO#{repo}",
+        "gsi1sk": "GHAS_ALERT#2026-06-16T00:00:00+00:00#g1",
+        "ghasAlertId": "g1",
+        "repository": repo,
+        "fetchedAt": "2026-06-16T00:00:00+00:00",
+    }
+
+
+def _patch_table(monkeypatch, table: _FakeTable) -> None:
+    monkeypatch.setattr(
+        "security_scanner.cli.commands.migrate.make_boto3_resource_and_client",
+        lambda config: (_FakeResource(table), object()),
+    )
+
+
+def test_dry_run_reports_inventory_without_mutating(monkeypatch, capsys):
+    table = _FakeTable([_legacy_finding(), _legacy_ghas()])
+    _patch_table(monkeypatch, table)
+
+    exit_code = main(
+        ["backfill-repo-axis", "--storage-backend", "dynamodb", "--dry-run"]
+    )
+
+    out = capsys.readouterr().out
+    assert exit_code == 0
+    assert "dry-run" in out
+    assert "FINDING: 1" in out
+    assert "GHAS_ALERT: 1" in out
+    assert "total legacy rows: 2" in out
+    assert table.update_calls == []  # no mutation
+
+
+def test_apply_backfills_and_reports_gate_clear(monkeypatch, capsys):
+    table = _FakeTable([_legacy_finding(), _legacy_ghas()])
+    _patch_table(monkeypatch, table)
+
+    exit_code = main(["backfill-repo-axis", "--storage-backend", "dynamodb"])
+
+    out = capsys.readouterr().out
+    assert exit_code == 0
+    assert "gate: CLEAR" in out
+    # both legacy rows updated in place to sharded keys
+    assert {(k["PK"], k["SK"]) for k in table.update_calls} == {
+        ("FINDING#f1", "META"),
+        ("GHAS_ALERT#g1", "META"),
+    }
+    for item in table.items:
+        assert item["repoAxisVersion"] == 2
+        assert "#SHARD#" in item["gsi1pk"]
+
+
+def test_apply_is_idempotent_second_run_clear_with_no_updates(monkeypatch, capsys):
+    table = _FakeTable([_legacy_finding(), _legacy_ghas()])
+    _patch_table(monkeypatch, table)
+
+    assert main(["backfill-repo-axis", "--storage-backend", "dynamodb"]) == 0
+    updates_after_first = len(table.update_calls)
+    capsys.readouterr()
+
+    exit_code = main(["backfill-repo-axis", "--storage-backend", "dynamodb"])
+    out = capsys.readouterr().out
+
+    assert exit_code == 0
+    assert "gate: CLEAR" in out
+    assert len(table.update_calls) == updates_after_first  # nothing left to backfill
+
+
+def test_rejects_non_dynamodb_backend(monkeypatch, capsys):
+    # must not even try to build a table for jsonl
+    called = False
+
+    def _boom(config):
+        nonlocal called
+        called = True
+        raise AssertionError("should not build a table for jsonl")
+
+    monkeypatch.setattr(
+        "security_scanner.cli.commands.migrate.make_boto3_resource_and_client", _boom
+    )
+
+    exit_code = main(["backfill-repo-axis", "--storage-backend", "jsonl"])
+
+    err = capsys.readouterr().err
+    assert exit_code == 2
+    assert "requires --storage-backend dynamodb" in err
+    assert called is False
+
+
+def test_apply_reports_gate_not_clear_on_failure(monkeypatch, capsys):
+    class _FailingTable(_FakeTable):
+        def update_item(self, **kwargs):
+            raise Exception("DynamoDB write failed")
+
+    table = _FailingTable([_legacy_finding()])
+    _patch_table(monkeypatch, table)
+
+    exit_code = main(["backfill-repo-axis", "--storage-backend", "dynamodb"])
+
+    out = capsys.readouterr().out
+    assert exit_code == 1
+    assert "gate: NOT CLEAR" in out