diff --git a/.changeset/cli-remove-migrate-package-exports.md b/.changeset/cli-remove-migrate-package-exports.md
new file mode 100644
index 0000000000..03ad1974d8
--- /dev/null
+++ b/.changeset/cli-remove-migrate-package-exports.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': minor
+---
+
+**BREAKING**: The `migrate package-exports` command has been removed. Use `repo fix` instead.
diff --git a/packages/cli/src/modules/build/lib/optionsParser.ts b/packages/cli/src/modules/build/lib/optionsParser.ts
index 45c7eac0aa..15561a2e42 100644
--- a/packages/cli/src/modules/build/lib/optionsParser.ts
+++ b/packages/cli/src/modules/build/lib/optionsParser.ts
@@ -62,8 +62,8 @@ export function createScriptOptionsParser(
     // Triggers the writing of options to the result object
     cmd.parseOptions(argsStr.split(' '));
 
-    (cmd as any)._storeOptionsAsProperties = currentOpts;
-    (cmd as any)._optionValues = currentStore;
+    (cmd as any)._optionValues = currentOpts;
+    (cmd as any)._storeOptionsAsProperties = currentStore;
 
     return result;
   };
diff --git a/packages/cli/src/modules/lint/lib/optionsParser.ts b/packages/cli/src/modules/lint/lib/optionsParser.ts
index 45c7eac0aa..15561a2e42 100644
--- a/packages/cli/src/modules/lint/lib/optionsParser.ts
+++ b/packages/cli/src/modules/lint/lib/optionsParser.ts
@@ -62,8 +62,8 @@ export function createScriptOptionsParser(
     // Triggers the writing of options to the result object
     cmd.parseOptions(argsStr.split(' '));
 
-    (cmd as any)._storeOptionsAsProperties = currentOpts;
-    (cmd as any)._optionValues = currentStore;
+    (cmd as any)._optionValues = currentOpts;
+    (cmd as any)._storeOptionsAsProperties = currentStore;
 
     return result;
   };