diff --git a/pkg/agent/config/config.go b/pkg/agent/config/config.go
index d061a14dc0..6f252be96c 100644
--- a/pkg/agent/config/config.go
+++ b/pkg/agent/config/config.go
@@ -530,6 +530,7 @@ func get(ctx context.Context, envInfo *cmds.Agent, proxy proxy.Proxy) (*config.N
 		}
 		nodeConfig.AgentConfig.CNIBinDir = filepath.Dir(hostLocal)
 		nodeConfig.AgentConfig.CNIConfDir = filepath.Join(envInfo.DataDir, "agent", "etc", "cni", "net.d")
+		nodeConfig.AgentConfig.FlannelCniConfFile = envInfo.FlannelCniConfFile
 	}
 
 	if !nodeConfig.Docker && nodeConfig.ContainerRuntimeEndpoint == "" {
diff --git a/pkg/agent/flannel/setup.go b/pkg/agent/flannel/setup.go
index a0174d5f95..fc21b51d52 100644
--- a/pkg/agent/flannel/setup.go
+++ b/pkg/agent/flannel/setup.go
@@ -91,7 +91,7 @@ const (
 )
 
 func Prepare(ctx context.Context, nodeConfig *config.Node) error {
-	if err := createCNIConf(nodeConfig.AgentConfig.CNIConfDir); err != nil {
+	if err := createCNIConf(nodeConfig.AgentConfig.CNIConfDir, nodeConfig); err != nil {
 		return err
 	}
 
@@ -146,12 +146,17 @@ func waitForPodCIDR(ctx context.Context, nodeName string, nodes typedcorev1.Node
 	return nil
 }
 
-func createCNIConf(dir string) error {
+func createCNIConf(dir string, nodeConfig *config.Node) error {
 	logrus.Debugf("Creating the CNI conf in directory %s", dir)
 	if dir == "" {
 		return nil
 	}
 	p := filepath.Join(dir, "10-flannel.conflist")
+
+	if nodeConfig.AgentConfig.FlannelCniConfFile != "" {
+		logrus.Debugf("Using %s as the flannel CNI conf", nodeConfig.AgentConfig.FlannelCniConfFile)
+		return util.CopyFile(nodeConfig.AgentConfig.FlannelCniConfFile, p)
+	}
 	return util.WriteFile(p, cniConf)
 }
 
diff --git a/pkg/agent/util/file.go b/pkg/agent/util/file.go
index 0cace178c7..17c263c143 100644
--- a/pkg/agent/util/file.go
+++ b/pkg/agent/util/file.go
@@ -16,3 +16,16 @@ func WriteFile(name string, content string) error {
 	}
 	return nil
 }
+
+func CopyFile(sourceFile string, destinationFile string) error {
+	os.MkdirAll(filepath.Dir(destinationFile), 0755)
+	input, err := ioutil.ReadFile(sourceFile)
+	if err != nil {
+		return errors.Wrapf(err, "copying %s to %s", sourceFile, destinationFile)
+	}
+	err = ioutil.WriteFile(destinationFile, input, 0644)
+	if err != nil {
+		return errors.Wrapf(err, "copying %s to %s", sourceFile, destinationFile)
+	}
+	return nil
+}
diff --git a/pkg/cli/cmds/agent.go b/pkg/cli/cmds/agent.go
index 90e1dac9ce..8da19df8af 100644
--- a/pkg/cli/cmds/agent.go
+++ b/pkg/cli/cmds/agent.go
@@ -31,6 +31,7 @@ type Agent struct {
 	NoFlannel                bool
 	FlannelIface             string
 	FlannelConf              string
+	FlannelCniConfFile       string
 	Debug                    bool
 	Rootless                 bool
 	RootlessAlreadyUnshared  bool
@@ -134,6 +135,11 @@ var (
 		Usage:       "(agent/networking) Override default flannel config file",
 		Destination: &AgentConfig.FlannelConf,
 	}
+	FlannelCniConfFileFlag = cli.StringFlag{
+		Name:        "flannel-cni-conf",
+		Usage:       "(agent/networking) Override default flannel cni config file",
+		Destination: &AgentConfig.FlannelCniConfFile,
+	}
 	ResolvConfFlag = cli.StringFlag{
 		Name:        "resolv-conf",
 		Usage:       "(agent/networking) Kubelet resolv.conf file",
@@ -259,6 +265,7 @@ func NewAgentCommand(action func(ctx *cli.Context) error) cli.Command {
 			ResolvConfFlag,
 			FlannelIfaceFlag,
 			FlannelConfFlag,
+			FlannelCniConfFileFlag,
 			ExtraKubeletArgs,
 			ExtraKubeProxyArgs,
 			ProtectKernelDefaultsFlag,
diff --git a/pkg/cli/cmds/server.go b/pkg/cli/cmds/server.go
index 09a60e5a73..12d1b866c3 100644
--- a/pkg/cli/cmds/server.go
+++ b/pkg/cli/cmds/server.go
@@ -439,6 +439,7 @@ var ServerFlags = []cli.Flag{
 	ResolvConfFlag,
 	FlannelIfaceFlag,
 	FlannelConfFlag,
+	FlannelCniConfFileFlag,
 	ExtraKubeletArgs,
 	ExtraKubeProxyArgs,
 	ProtectKernelDefaultsFlag,
diff --git a/pkg/daemons/config/types.go b/pkg/daemons/config/types.go
index 21389ec14c..237a2f2474 100644
--- a/pkg/daemons/config/types.go
+++ b/pkg/daemons/config/types.go
@@ -111,6 +111,7 @@ type Agent struct {
 	ImageCredProvBinDir     string
 	ImageCredProvConfig     string
 	IPSECPSK                string
+	FlannelCniConfFile      string
 	StrongSwanDir           string
 	PrivateRegistry         string
 	SystemDefaultRegistry   string