diff --git a/pkg/neg/manager.go b/pkg/neg/manager.go
index d236f5a1c..4e7e66203 100644
--- a/pkg/neg/manager.go
+++ b/pkg/neg/manager.go
@@ -21,6 +21,7 @@ import (
 	"fmt"
 	"net/http"
 	"reflect"
+	"slices"
 	"sync"
 	"time"
 
@@ -615,6 +616,7 @@ func (manager *syncerManager) processNEGDeletionCandidate(svcNegCR *negv1beta1.S
 	var errList []error
 	shouldDeleteNegCR := true
 	deleteByZone := len(svcNegCR.Status.NetworkEndpointGroups) == 0
+	var deletedNegRefIds []string
 
 	for _, negRef := range svcNegCR.Status.NetworkEndpointGroups {
 		resourceID, err := cloud.ParseResourceURL(negRef.SelfLink)
@@ -623,10 +625,20 @@ func (manager *syncerManager) processNEGDeletionCandidate(svcNegCR *negv1beta1.S
 			deleteByZone = true
 			continue
 		}
+		deletedNegRefIds = append(deletedNegRefIds, negRef.Id)
 
 		shouldDeleteNegCR = shouldDeleteNegCR && manager.deleteNegOrReportErr(resourceID.Key.Name, resourceID.Key.Zone, svcNegCR, &errList)
 	}
 
+	// Clear NEG Refs for those that has been successfully deleted.
+	var newNegRef []negv1beta1.NegObjectReference
+	for _, negRef := range svcNegCR.Status.NetworkEndpointGroups {
+		if !slices.Contains(deletedNegRefIds, negRef.Id) {
+			newNegRef = append(newNegRef, negRef)
+		}
+	}
+	svcNegCR.Status.NetworkEndpointGroups = newNegRef
+
 	if deleteByZone {
 		manager.logger.V(2).Info("Deletion candidate has 0 NEG reference", "svcneg", klog.KObj(svcNegCR), "svcNegCR", svcNegCR)
 		for _, zone := range zones {