diff --git a/pkg/agent/flowexporter/connections/connections.go b/pkg/agent/flowexporter/connections/connections.go
index c76aadddab6..80061a9991b 100644
--- a/pkg/agent/flowexporter/connections/connections.go
+++ b/pkg/agent/flowexporter/connections/connections.go
@@ -77,6 +77,19 @@ func (cs *connectionStore) ForAllConnectionsDo(callback flowexporter.ConnectionM
 	return nil
 }
 
+// ForAllConnectionsDoWithoutLock execute the callback for each connection in connection
+// map, without grabbing the lock. Caller is expected to grab lock.
+func (cs *connectionStore) ForAllConnectionsDoWithoutLock(callback flowexporter.ConnectionMapCallBack) error {
+	for k, v := range cs.connections {
+		err := callback(k, v)
+		if err != nil {
+			klog.Errorf("Callback execution failed for flow with key: %v, conn: %v, k, v: %v", k, v, err)
+			return err
+		}
+	}
+	return nil
+}
+
 // AddConnToMap adds the connection to connections map given connection key.
 // This is used only for unit tests.
 func (cs *connectionStore) AddConnToMap(connKey *flowexporter.ConnectionKey, conn *flowexporter.Connection) {
diff --git a/pkg/agent/flowexporter/connections/conntrack_connections.go b/pkg/agent/flowexporter/connections/conntrack_connections.go
index a573057cb6e..dc307f78478 100644
--- a/pkg/agent/flowexporter/connections/conntrack_connections.go
+++ b/pkg/agent/flowexporter/connections/conntrack_connections.go
@@ -116,7 +116,10 @@ func (cs *ConntrackConnectionStore) Poll() ([]int, error) {
 		return nil
 	}
 
-	if err := cs.ForAllConnectionsDo(deleteIfStaleOrResetConn); err != nil {
+	// Hold the lock until verify whether the connection exist in conntrack table.
+	cs.AcquireConnStoreLock()
+
+	if err := cs.ForAllConnectionsDoWithoutLock(deleteIfStaleOrResetConn); err != nil {
 		return []int{}, err
 	}
 
@@ -149,6 +152,9 @@ func (cs *ConntrackConnectionStore) Poll() ([]int, error) {
 		}
 		connsLens = append(connsLens, len(filteredConnsList))
 	}
+
+	cs.ReleaseConnStoreLock()
+
 	metrics.TotalConnectionsInConnTrackTable.Set(float64(totalConns))
 	maxConns, err := cs.connDumper.GetMaxConnections()
 	if err != nil {
@@ -203,13 +209,12 @@ func (cs *ConntrackConnectionStore) addNetworkPolicyMetadata(conn *flowexporter.
 // AddOrUpdateConn updates the connection if it is already present, i.e., update timestamp, counters etc.,
 // or adds a new connection with the resolved K8s metadata.
 func (cs *ConntrackConnectionStore) AddOrUpdateConn(conn *flowexporter.Connection) {
+	conn.IsPresent = true
 	connKey := flowexporter.NewConnectionKey(conn)
-	cs.mutex.Lock()
-	defer cs.mutex.Unlock()
 
 	existingConn, exists := cs.connections[connKey]
 	if exists {
-		existingConn.IsPresent = true
+		existingConn.IsPresent = conn.IsPresent
 		if flowexporter.IsConnectionDying(existingConn) {
 			return
 		}
diff --git a/test/e2e/framework.go b/test/e2e/framework.go
index 206e224e55e..95c82be976b 100644
--- a/test/e2e/framework.go
+++ b/test/e2e/framework.go
@@ -126,6 +126,7 @@ const (
 
 	nginxLBService = "nginx-loadbalancer"
 
+	connectionStorePollingInterval      = 1 * time.Second
 	exporterActiveFlowExportTimeout     = 2 * time.Second
 	exporterIdleFlowExportTimeout       = 1 * time.Second
 	aggregatorActiveFlowRecordTimeout   = 3500 * time.Millisecond
@@ -694,7 +695,7 @@ func (data *TestData) enableAntreaFlowExporter(ipfixCollector string) error {
 	// Enable flow exporter feature and add related config params to antrea agent configmap.
 	ac := func(config *agentconfig.AgentConfig) {
 		config.FeatureGates["FlowExporter"] = true
-		config.FlowPollInterval = "1s"
+		config.FlowPollInterval = connectionStorePollingInterval.String()
 		config.ActiveFlowExportTimeout = exporterActiveFlowExportTimeout.String()
 		config.IdleFlowExportTimeout = exporterIdleFlowExportTimeout.String()
 		if ipfixCollector != "" {