diff --git a/pkg/agent/flannel/flannel.go b/pkg/agent/flannel/flannel.go
index 26b2950c01..87973d9f52 100644
--- a/pkg/agent/flannel/flannel.go
+++ b/pkg/agent/flannel/flannel.go
@@ -68,8 +68,10 @@ func flannel(ctx context.Context, flannelIface *net.Interface, flannelConf, kube
 		return err
 	}
 
-	go network.SetupAndEnsureIPTables(network.MasqRules(config.Network, bn.Lease()), 60)
-	go network.SetupAndEnsureIPTables(network.ForwardRules(config.Network.String()), 50)
+	if netMode == (ipv4+ipv6) || netMode == ipv4 {
+		go network.SetupAndEnsureIPTables(network.MasqRules(config.Network, bn.Lease()), 60)
+		go network.SetupAndEnsureIPTables(network.ForwardRules(config.Network.String()), 50)
+	}
 
 	if flannelIPv6Masq && config.IPv6Network.String() != emptyIPv6Network {
 		logrus.Debugf("Creating IPv6 masquerading iptables rules for %s network", config.IPv6Network.String())
@@ -77,7 +79,7 @@ func flannel(ctx context.Context, flannelIface *net.Interface, flannelConf, kube
 		go network.SetupAndEnsureIP6Tables(network.ForwardRules(config.IPv6Network.String()), 50)
 	}
 
-	if err := WriteSubnetFile(subnetFile, config.Network, config.IPv6Network, true, bn); err != nil {
+	if err := WriteSubnetFile(subnetFile, config.Network, config.IPv6Network, true, bn, netMode); err != nil {
 		// Continue, even though it failed.
 		logrus.Warningf("Failed to write flannel subnet file: %s", err)
 	} else {
@@ -97,8 +99,14 @@ func LookupExtInterface(iface *net.Interface, netMode int) (*backend.ExternalInt
 
 	if iface == nil {
 		logrus.Debug("No interface defined for flannel in the config. Fetching the default gateway interface")
-		if iface, err = ip.GetDefaultGatewayInterface(); err != nil {
-			return nil, fmt.Errorf("failed to get default interface: %s", err)
+		if netMode == ipv4 || netMode == (ipv4+ipv6) {
+			if iface, err = ip.GetDefaultGatewayInterface(); err != nil {
+				return nil, fmt.Errorf("failed to get default interface: %s", err)
+			}
+		} else {
+			if iface, err = ip.GetDefaultV6GatewayInterface(); err != nil {
+				return nil, fmt.Errorf("failed to get default interface: %s", err)
+			}
 		}
 	}
 	logrus.Debugf("The interface %s will be used by flannel", iface.Name)
@@ -147,7 +155,7 @@ func LookupExtInterface(iface *net.Interface, netMode int) (*backend.ExternalInt
 	}, nil
 }
 
-func WriteSubnetFile(path string, nw ip.IP4Net, nwv6 ip.IP6Net, ipMasq bool, bn backend.Network) error {
+func WriteSubnetFile(path string, nw ip.IP4Net, nwv6 ip.IP6Net, ipMasq bool, bn backend.Network, netMode int) error {
 	dir, name := filepath.Split(path)
 	os.MkdirAll(dir, 0755)
 
@@ -161,9 +169,10 @@ func WriteSubnetFile(path string, nw ip.IP4Net, nwv6 ip.IP6Net, ipMasq bool, bn
 	// sn.IP by one
 	sn := bn.Lease().Subnet
 	sn.IP++
-
-	fmt.Fprintf(f, "FLANNEL_NETWORK=%s\n", nw)
-	fmt.Fprintf(f, "FLANNEL_SUBNET=%s\n", sn)
+	if netMode == ipv4 || netMode == (ipv4+ipv6) {
+		fmt.Fprintf(f, "FLANNEL_NETWORK=%s\n", nw)
+		fmt.Fprintf(f, "FLANNEL_SUBNET=%s\n", sn)
+	}
 
 	if nwv6.String() != emptyIPv6Network {
 		snv6 := bn.Lease().IPv6Subnet
diff --git a/pkg/agent/flannel/setup.go b/pkg/agent/flannel/setup.go
index 18065c185e..180578f7e7 100644
--- a/pkg/agent/flannel/setup.go
+++ b/pkg/agent/flannel/setup.go
@@ -45,7 +45,8 @@ const (
 
 	flannelConf = `{
 	"Network": "%CIDR%",
-	"EnableIPv6": %DUALSTACK%,
+	"EnableIPv6": %IPV6_ENABLED%,
+	"EnableIPv4": %IPV4_ENABLED%,
 	"IPv6Network": "%CIDR_IPV6%",
 	"Backend": %backend%
 }
@@ -140,6 +141,7 @@ func createCNIConf(dir string) error {
 }
 
 func createFlannelConf(nodeConfig *config.Node) error {
+	var ipv4Enabled string
 	logrus.Debugf("Creating the flannel configuration for backend %s in file %s", nodeConfig.FlannelBackend, nodeConfig.FlannelConfFile)
 	if nodeConfig.FlannelConfFile == "" {
 		return errors.New("Flannel configuration not defined")
@@ -148,7 +150,40 @@ func createFlannelConf(nodeConfig *config.Node) error {
 		logrus.Infof("Using custom flannel conf defined at %s", nodeConfig.FlannelConfFile)
 		return nil
 	}
-	confJSON := strings.ReplaceAll(flannelConf, "%CIDR%", nodeConfig.AgentConfig.ClusterCIDR.String())
+	netMode, err := findNetMode(nodeConfig.AgentConfig.ClusterCIDRs)
+	if err != nil {
+		logrus.Fatalf("Flannel error checking netMode: %v", err)
+		return err
+	}
+	if netMode == ipv4 || netMode == (ipv4+ipv6) {
+		ipv4Enabled = "true"
+	} else {
+		ipv4Enabled = "false"
+	}
+	confJSON := strings.ReplaceAll(flannelConf, "%IPV4_ENABLED%", ipv4Enabled)
+	if netMode == ipv4 {
+		confJSON = strings.ReplaceAll(confJSON, "%CIDR%", nodeConfig.AgentConfig.ClusterCIDR.String())
+		confJSON = strings.ReplaceAll(confJSON, "%IPV6_ENABLED%", "false")
+		confJSON = strings.ReplaceAll(confJSON, "%CIDR_IPV6%", emptyIPv6Network)
+	} else if netMode == (ipv4 + ipv6) {
+		confJSON = strings.ReplaceAll(confJSON, "%CIDR%", nodeConfig.AgentConfig.ClusterCIDR.String())
+		confJSON = strings.ReplaceAll(confJSON, "%IPV6_ENABLED%", "true")
+		for _, cidr := range nodeConfig.AgentConfig.ClusterCIDRs {
+			if utilsnet.IsIPv6(cidr.IP) {
+				// Only one ipv6 range available. This might change in future: https://github.com/kubernetes/enhancements/issues/2593
+				confJSON = strings.ReplaceAll(confJSON, "%CIDR_IPV6%", cidr.String())
+			}
+		}
+	} else {
+		confJSON = strings.ReplaceAll(confJSON, "%CIDR%", "0.0.0.0/0")
+		confJSON = strings.ReplaceAll(confJSON, "%IPV6_ENABLED%", "true")
+		for _, cidr := range nodeConfig.AgentConfig.ClusterCIDRs {
+			if utilsnet.IsIPv6(cidr.IP) {
+				// Only one ipv6 range available. This might change in future: https://github.com/kubernetes/enhancements/issues/2593
+				confJSON = strings.ReplaceAll(confJSON, "%CIDR_IPV6%", cidr.String())
+			}
+		}
+	}
 
 	var backendConf string
 
@@ -169,25 +204,6 @@ func createFlannelConf(nodeConfig *config.Node) error {
 	}
 	confJSON = strings.ReplaceAll(confJSON, "%backend%", backendConf)
 
-	netMode, err := findNetMode(nodeConfig.AgentConfig.ClusterCIDRs)
-	if err != nil {
-		logrus.Fatalf("Flannel error checking netMode: %v", err)
-		return err
-	}
-
-	if netMode == (ipv4 + ipv6) {
-		confJSON = strings.ReplaceAll(confJSON, "%DUALSTACK%", "true")
-		for _, cidr := range nodeConfig.AgentConfig.ClusterCIDRs {
-			if utilsnet.IsIPv6(cidr.IP) {
-				// Only one ipv6 range available. This might change in future: https://github.com/kubernetes/enhancements/issues/2593
-				confJSON = strings.ReplaceAll(confJSON, "%CIDR_IPV6%", cidr.String())
-			}
-		}
-	} else {
-		confJSON = strings.ReplaceAll(confJSON, "%DUALSTACK%", "false")
-		confJSON = strings.ReplaceAll(confJSON, "%CIDR_IPV6%", emptyIPv6Network)
-	}
-
 	logrus.Debugf("The flannel configuration is %s", confJSON)
 	return util.WriteFile(nodeConfig.FlannelConfFile, confJSON)
 }
diff --git a/pkg/cli/server/server.go b/pkg/cli/server/server.go
index 829a608d6b..45e411dda9 100644
--- a/pkg/cli/server/server.go
+++ b/pkg/cli/server/server.go
@@ -534,9 +534,6 @@ func validateNetworkConfiguration(serverConfig server.Config) error {
 		if serverConfig.ControlConfig.DisableNPC == false {
 			return errors.New("network policy enforcement is not compatible with IPv6 only operation; server must be restarted with --disable-network-policy")
 		}
-		if serverConfig.ControlConfig.FlannelBackend != config.FlannelBackendNone {
-			return errors.New("Flannel is not compatible with IPv6 only operation; server must be restarted with --flannel-backend=none")
-		}
 	}
 
 	return nil