diff --git a/CHANGELOG.md b/CHANGELOG.md
index 77fc344..550fa2b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.6.5] - 2026-03-24
+### Fixed
+- Fixed an issue where client-side flags could override server-side flags.
+  - Client-side overrides now need an explicit enablement flag: `AllowFlagsOverride`
+
 ## [1.6.4] - 2026-03-23
 ### Added
 - Add support for single worker scan timeout HTTP response handling (504)
@@ -200,3 +205,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 [1.6.2]: https://github.com/scanoss/api.go/compare/v1.6.1...v1.6.2
 [1.6.3]: https://github.com/scanoss/api.go/compare/v1.6.2...v1.6.3
 [1.6.4]: https://github.com/scanoss/api.go/compare/v1.6.3...v1.6.4
+[1.6.5]: https://github.com/scanoss/api.go/compare/v1.6.4...v1.6.5
diff --git a/config/app-config-prod.json b/config/app-config-prod.json
index de38f89..d990fae 100644
--- a/config/app-config-prod.json
+++ b/config/app-config-prod.json
@@ -25,6 +25,7 @@
     "ScanBinary": "scanoss",
     "ScanDebug": false,
     "ScanFlags": 0,
+    "AllowFlagsOverride": false,
     "ScanTimeout": 180,
     "WfpGrouping": 3,
     "Workers": 2,
diff --git a/pkg/config/server_config.go b/pkg/config/server_config.go
index b15cdec..56e0118 100644
--- a/pkg/config/server_config.go
+++ b/pkg/config/server_config.go
@@ -59,6 +59,7 @@ type ServerConfig struct {
 		ScanKbName         string `env:"SCAN_KB_NAME"`                 // KB name passed as "-n" parameter to the scanoss command
 		ScanDebug          bool   `env:"SCAN_DEBUG"`                   // true/false
 		ScanFlags          int    `env:"SCAN_ENGINE_FLAGS"`            // Default flags to use when scanning
+		AllowFlagsOverride bool   `env:"SCAN_ALLOW_FLAGS_OVERRIDE"`    // Allow clients to override the default flags
 		ScanTimeout        int    `env:"SCAN_ENGINE_TIMEOUT"`          // timeout for waiting for the scan engine to respond
 		WfpGrouping        int    `env:"SCAN_WFP_GROUPING"`            // number of WFP to group into a single scan engine command
 		Workers            int    `env:"SCAN_WORKERS"`                 // Number of concurrent workers to use per scan request
@@ -138,6 +139,7 @@ func setServerConfigDefaults(cfg *ServerConfig) {
 	cfg.Scanning.MinSnippetHits = 0         // Lets the engine decide on minimum snippet hits based on the file total lines
 	cfg.Scanning.MinSnippetLines = 0        // Lets the engine decide on minimum snippet hits on the file total lines
 	cfg.Scanning.HonourFileExts = true
+	cfg.Scanning.AllowFlagsOverride = false // Disallow clients overriding the default flags if it's set server-side
 }
 
 // LoadFile loads the specified file and returns its contents in a string array.
diff --git a/pkg/service/scanning_service.go b/pkg/service/scanning_service.go
index 985a9d8..1cdb5bb 100644
--- a/pkg/service/scanning_service.go
+++ b/pkg/service/scanning_service.go
@@ -184,6 +184,16 @@ func (s APIService) getConfigFromRequest(r *http.Request, zs *zap.SugaredLogger)
 	if len(dbName) == 0 {
 		dbName = strings.TrimSpace(r.Header.Get("db_name"))
 	}
+	if len(flags) > 0 && s.config.Scanning.ScanFlags > 0 {
+		if !s.config.Scanning.AllowFlagsOverride {
+			zs.Warnf("Ignoring flags (%v) in the request. Using flags from the server config: %v",
+				flags, s.config.Scanning.ScanFlags)
+			flags = "" // Clear the flags to use the server configuration
+		} else {
+			zs.Debugf("Using flags (%v) from the request instead of server config: %v",
+				flags, s.config.Scanning.ScanFlags)
+		}
+	}
 	scanSettings := strings.TrimSpace(r.Header.Get("scanoss-settings")) // Check the header for scan settings
 	if s.config.App.Trace {
 		zs.Debugf("Header: %v, Form: %v, flags: %v, type: %v, assets: %v, db_name: %v, scanSettings: %v",
diff --git a/pkg/service/scanning_service_test.go b/pkg/service/scanning_service_test.go
index 21c845f..db068cd 100644
--- a/pkg/service/scanning_service_test.go
+++ b/pkg/service/scanning_service_test.go
@@ -601,3 +601,75 @@ func TestScanDirectSingleSlow(t *testing.T) {
 		})
 	}
 }
+
+func TestScanFlags(t *testing.T) {
+	err := zlog.NewSugaredDevLogger()
+	if err != nil {
+		t.Fatalf("an error '%s' was not expected when opening a sugared logger", err)
+	}
+	defer zlog.SyncZap()
+	myConfig := setupConfig(t)
+	myConfig.App.Trace = true
+	myConfig.Scanning.ScanDebug = true
+	myConfig.Scanning.ScanTimeout = 5
+
+	tests := []struct {
+		name               string
+		serverFlags        int
+		allowFlagsOverride bool
+		clientFlags        string
+		want               int
+	}{
+		{
+			name:               "Scanning - no flags",
+			serverFlags:        0,
+			allowFlagsOverride: false,
+			clientFlags:        "",
+			want:               0,
+		},
+		{
+			name:               "Scanning - client flags",
+			serverFlags:        0,
+			allowFlagsOverride: false,
+			clientFlags:        "256",
+			want:               256,
+		},
+		{
+			name:               "Scanning - server flags",
+			serverFlags:        1248,
+			allowFlagsOverride: false,
+			clientFlags:        "",
+			want:               1248,
+		},
+		{
+			name:               "Scanning - server/clients flags - allowed",
+			serverFlags:        1248,
+			allowFlagsOverride: true,
+			clientFlags:        "256",
+			want:               256,
+		},
+		{
+			name:               "Scanning - server/clients flags - not allowed",
+			serverFlags:        1248,
+			allowFlagsOverride: false,
+			clientFlags:        "256",
+			want:               1248,
+		},
+	}
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			myConfig.Scanning.ScanFlags = test.serverFlags
+			myConfig.Scanning.AllowFlagsOverride = test.allowFlagsOverride
+
+			req := httptest.NewRequest(http.MethodPost, "/scan/direct", nil)
+			if len(test.clientFlags) > 0 {
+				req.Header.Add("flags", test.clientFlags)
+			}
+			apiService := NewAPIService(myConfig)
+			cfg, err := apiService.getConfigFromRequest(req, zlog.S)
+			assert.NoError(t, err)
+			assert.Equal(t, test.want, cfg.flags)
+			fmt.Println("Flags: ", cfg.flags)
+		})
+	}
+}