diff --git a/src/util/config.ts b/src/util/config.ts
index c53031b78..6b866b654 100644
--- a/src/util/config.ts
+++ b/src/util/config.ts
@@ -1,5 +1,5 @@
 import micromatch from 'micromatch';
-import type { ImportedConfiguration, LocalConfiguration, Configuration, IssueType } from '../types';
+import type { ImportedConfiguration, LocalConfiguration, Configuration, IssueType, Report } from '../types';
 
 export const resolveConfig = (
   importedConfiguration: ImportedConfiguration,
@@ -41,14 +41,18 @@ export const resolveIncludedIssueTypes = (
   // Automatically inject the devDependencies report type in dev mode
   const deps: IssueType[] = resolvedConfig?.dev ? ['dependencies', 'devDependencies'] : ['dependencies'];
   const groups: IssueType[] = ['files', ...deps, 'unlisted', 'exports', 'types', 'nsExports', 'nsTypes', 'duplicates'];
-  const include = [includeArg, resolvedConfig?.include ?? []]
-    .flat()
-    .map(value => value.split(','))
-    .flat();
-  const exclude = [excludeArg, resolvedConfig?.exclude ?? []]
-    .flat()
-    .map(value => value.split(','))
-    .flat();
-  const includes = (include.length > 0 ? include : groups).filter(group => !exclude.includes(group));
-  return groups.reduce((r, group) => ((r[group] = includes.includes(group)), r), {} as Configuration['report']);
+
+  // Allow space-separated argument values (--include files,dependencies)
+  const normalizedIncludesArg = includeArg.map(value => value.split(',')).flat();
+  const normalizedExcludesArg = excludeArg.map(value => value.split(',')).flat();
+
+  // CLI arguments override local options
+  const excludes = (resolvedConfig?.exclude ?? []).filter(exclude => !normalizedIncludesArg.includes(exclude));
+  const includes = (resolvedConfig?.include ?? []).filter(include => !normalizedExcludesArg.includes(include));
+
+  const include = [normalizedIncludesArg, includes].flat();
+  const exclude = [normalizedExcludesArg, excludes].flat();
+  const included = (include.length > 0 ? include : groups).filter(group => !exclude.includes(group));
+
+  return groups.reduce((types, group) => ((types[group] = included.includes(group)), types), {} as Report);
 };