Two fixes:

* Consider that the @WebService annotation (et al) can be in a supertype or interface

* getARemoteMethod should only return public methods, since protected, package-private, and private methods are not exposed

java/ql/lib/semmle/code/java/frameworks/JaxWS.qll

@@ -25,7 +25,7 @@ string getAJaxRsPackage(string subpackage) { result = getAJaxRsPackage() + "." +
  */
 class JaxWsEndpoint extends Class {
   JaxWsEndpoint() {
-    exists(AnnotationType a | a = this.getAnAnnotation().getType() |
+    exists(AnnotationType a | a = this.getAnAncestor().getAnAnnotation().getType() |
       a.hasName(["WebService", "WebServiceProvider", "WebServiceClient"])
     )
   }
@@ -37,6 +37,7 @@ class JaxWsEndpoint extends Class {
    */
   Method getARemoteMethod() {
     result = this.getACallable() and
+    result.isPublic() and
     not result instanceof InitializerMethod and
     not exists(Annotation a | a = result.getAnAnnotation() |
       a.getType().hasQualifiedName(["javax", "jakarta"] + ".jws", "WebMethod") and

java/ql/test/library-tests/frameworks/JaxWs/JaxWsEndpoint.java

@@ -11,27 +11,27 @@ import javax.xml.ws.WebServiceProvider;
 class WebServiceClass { // $ JaxWsEndpoint
 
   @WebMethod
-  void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
   @WebEndpoint
-  void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
-  String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
+  public String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }
 
-  String unacceptableParamType(File param) { // not an endpoint
+  public String unacceptableParamType(File param) { // not an endpoint
     return null;
   }
 
-  File unacceptableReturnType() { // not an endpoint
+  public File unacceptableReturnType() { // not an endpoint
     return null;
   }
 
   @XmlJavaTypeAdapter
-  File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
+  public File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }
 }
@@ -41,27 +41,27 @@ class WebServiceClass { // $ JaxWsEndpoint
 class WebServiceProviderClass { // $ JaxWsEndpoint
 
   @WebMethod
-  void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
   @WebEndpoint
-  void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
-  String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
+  public String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }
 
-  String unacceptableParamType(File param) { // not an endpoint
+  public String unacceptableParamType(File param) { // not an endpoint
     return null;
   }
 
-  File unacceptableReturnType() { // not an endpoint
+  public File unacceptableReturnType() { // not an endpoint
     return null;
   }
 
   @XmlJavaTypeAdapter
-  File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
+  public File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }
 }
@@ -71,27 +71,27 @@ class WebServiceProviderClass { // $ JaxWsEndpoint
 class WebServiceClientClass { // $ JaxWsEndpoint
 
   @WebMethod
-  void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebMethodMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
   @WebEndpoint
-  void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
+  public void WebEndpointMethod() { // $ JaxWsEndpointRemoteMethod
   }
 
-  String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
+  public String acceptableTypes(String param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }
 
-  String unacceptableParamType(File param) { // not an endpoint
+  public String unacceptableParamType(File param) { // not an endpoint
     return null;
   }
 
-  File unacceptableReturnType() { // not an endpoint
+  public File unacceptableReturnType() { // not an endpoint
     return null;
   }
 
   @XmlJavaTypeAdapter
-  File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
+  public File annotatedTypes(@XmlJavaTypeAdapter File param) { // $ JaxWsEndpointRemoteMethod
     return null;
   }