diff --git a/pkg/iac/rego/load.go b/pkg/iac/rego/load.go
index a1c29d163fae..8f1033ecfa2d 100644
--- a/pkg/iac/rego/load.go
+++ b/pkg/iac/rego/load.go
@@ -295,6 +295,12 @@ func (s *Scanner) filterModules(retriever *MetadataRetriever) error {
 			continue
 		}
 
+		if IsBuiltinNamespace(getModuleNamespace(module)) {
+			if _, disabled := s.disabledCheckIDs[meta.ID]; disabled { // ignore builtin disabled checks
+				continue
+			}
+		}
+
 		if len(meta.InputOptions.Selectors) == 0 {
 			s.logger.Warn(
 				"Module has no input selectors - it will be loaded for all inputs!",
diff --git a/pkg/iac/rego/options.go b/pkg/iac/rego/options.go
index d4b622a68c16..5cc60284abdb 100644
--- a/pkg/iac/rego/options.go
+++ b/pkg/iac/rego/options.go
@@ -106,3 +106,14 @@ func WithCustomSchemas(schemas map[string][]byte) options.ScannerOption {
 		}
 	}
 }
+
+// WithDisabledCheckIDs disables checks by their ID (ID field in metadata)
+func WithDisabledCheckIDs(ids ...string) options.ScannerOption {
+	return func(s options.ConfigurableScanner) {
+		if ss, ok := s.(*Scanner); ok {
+			for _, id := range ids {
+				ss.disabledCheckIDs[id] = struct{}{}
+			}
+		}
+	}
+}
diff --git a/pkg/iac/rego/scanner.go b/pkg/iac/rego/scanner.go
index a8e1caf525b3..9cf80fc83da0 100644
--- a/pkg/iac/rego/scanner.go
+++ b/pkg/iac/rego/scanner.go
@@ -69,6 +69,8 @@ type Scanner struct {
 	embeddedLibs   map[string]*ast.Module
 	embeddedChecks map[string]*ast.Module
 	customSchemas  map[string][]byte
+
+	disabledCheckIDs map[string]struct{}
 }
 
 func (s *Scanner) SetIncludeDeprecatedChecks(b bool) {
@@ -109,12 +111,13 @@ func NewScanner(source types.Source, opts ...options.ScannerOption) *Scanner {
 	}
 
 	s := &Scanner{
-		regoErrorLimit: ast.CompileErrorLimitDefault,
-		sourceType:     source,
-		ruleNamespaces: make(map[string]struct{}),
-		runtimeValues:  addRuntimeValues(),
-		logger:         log.WithPrefix("rego"),
-		customSchemas:  make(map[string][]byte),
+		regoErrorLimit:   ast.CompileErrorLimitDefault,
+		sourceType:       source,
+		ruleNamespaces:   make(map[string]struct{}),
+		runtimeValues:    addRuntimeValues(),
+		logger:           log.WithPrefix("rego"),
+		customSchemas:    make(map[string][]byte),
+		disabledCheckIDs: make(map[string]struct{}),
 	}
 
 	maps.Copy(s.ruleNamespaces, builtinNamespaces)
diff --git a/pkg/iac/rego/scanner_test.go b/pkg/iac/rego/scanner_test.go
index 73ef55223f14..1310e56d2ec4 100644
--- a/pkg/iac/rego/scanner_test.go
+++ b/pkg/iac/rego/scanner_test.go
@@ -1153,3 +1153,87 @@ deny {
 		})
 	}
 }
+
+func Test_RegoScanner_WithDisabledCheckIDs(t *testing.T) {
+
+	check := `# METADATA
+# custom:
+#   id: TEST-001
+#   avd_id: AVD-TEST-001
+#   severity: LOW
+#   provider: aws
+#   service: s3
+#   short_code: test
+package builtin.test
+
+deny {
+  true
+}
+`
+
+	tests := []struct {
+		name           string
+		disabledChecks []string
+		inputCheck     string
+		expected       bool
+	}{
+		{
+			name:       "no disabled checks",
+			expected:   true,
+			inputCheck: check,
+		},
+		{
+			name:           "disable check by ID",
+			disabledChecks: []string{"TEST-001"},
+			inputCheck:     check,
+		},
+		{
+			name:           "disabling a non-existent check",
+			disabledChecks: []string{"FOO"},
+			expected:       true,
+			inputCheck:     check,
+		},
+		{
+			name:           "one of the identifiers does not exist",
+			disabledChecks: []string{"FOO", "TEST-001"},
+			inputCheck:     check,
+		},
+		{
+			name: "do not disable user checks with builtin IDs",
+			inputCheck: `# METADATA
+# custom:
+#   id: TEST-001
+#   avd_id: AVD-TEST-001
+#   severity: LOW
+#   provider: aws
+#   service: s3
+#   short_code: test
+package user.test
+
+deny {
+  true
+}
+`,
+			disabledChecks: []string{"TEST-001"},
+			expected:       true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+
+			scanner := rego.NewScanner(
+				types.SourceYAML,
+				rego.WithPolicyReader(strings.NewReader(tt.inputCheck)),
+				rego.WithDisabledCheckIDs(tt.disabledChecks...),
+				rego.WithPolicyNamespaces("user"),
+			)
+
+			require.NoError(t, scanner.LoadPolicies(nil))
+			results, err := scanner.ScanInput(context.TODO(), rego.Input{})
+			require.NoError(t, err)
+
+			require.Equal(t, tt.expected, len(results.GetFailed()) > 0)
+		})
+	}
+}