diff --git a/cmake/onnxruntime_java_unittests.cmake b/cmake/onnxruntime_java_unittests.cmake
index 8edf61065d6a..6038532d9217 100644
--- a/cmake/onnxruntime_java_unittests.cmake
+++ b/cmake/onnxruntime_java_unittests.cmake
@@ -1,23 +1,31 @@
 # Copyright (c) 2019, 2022, Oracle and/or its affiliates. All rights reserved.
 # Licensed under the MIT License.
 
-# This is a windows only file so we can run gradle tests via ctest
+# This is a helper script that enables us to run gradle tests via ctest.
+
 FILE(TO_NATIVE_PATH ${GRADLE_EXECUTABLE} GRADLE_NATIVE_PATH)
 FILE(TO_NATIVE_PATH ${BIN_DIR} BINDIR_NATIVE_PATH)
 
-message(STATUS "GRADLE_TEST_EP_FLAGS: ${ORT_PROVIDER_FLAGS}")
-if (onnxruntime_ENABLE_TRAINING_APIS)
-    message(STATUS "Running ORT Java training tests")
-    execute_process(COMMAND cmd /C ${GRADLE_NATIVE_PATH} --console=plain cmakeCheck -DcmakeBuildDir=${BINDIR_NATIVE_PATH} -Dorg.gradle.daemon=false ${ORT_PROVIDER_FLAGS} -DENABLE_TRAINING_APIS=1
-      WORKING_DIRECTORY ${REPO_ROOT}/java
-      RESULT_VARIABLE HAD_ERROR)
-else()
-    execute_process(COMMAND cmd /C ${GRADLE_NATIVE_PATH} --console=plain cmakeCheck -DcmakeBuildDir=${BINDIR_NATIVE_PATH} -Dorg.gradle.daemon=false ${ORT_PROVIDER_FLAGS}
-      WORKING_DIRECTORY ${REPO_ROOT}/java
-      RESULT_VARIABLE HAD_ERROR)
+message(STATUS "gradle additional system property definitions: ${GRADLE_SYSTEM_PROPERTY_DEFINITIONS}")
+
+set(GRADLE_TEST_ARGS
+    ${GRADLE_NATIVE_PATH}
+    cmakeCheck
+    --console=plain
+    -DcmakeBuildDir=${BINDIR_NATIVE_PATH}
+    -Dorg.gradle.daemon=false
+    ${GRADLE_SYSTEM_PROPERTY_DEFINITIONS})
+
+if(WIN32)
+  list(PREPEND GRADLE_TEST_ARGS cmd /C)
 endif()
 
+message(STATUS "gradle test command args: ${GRADLE_TEST_ARGS}")
+
+execute_process(COMMAND ${GRADLE_TEST_ARGS}
+    WORKING_DIRECTORY ${REPO_ROOT}/java
+    RESULT_VARIABLE HAD_ERROR)
 
 if(HAD_ERROR)
-    message(FATAL_ERROR "Java Unitests failed")
+  message(FATAL_ERROR "Java Unitests failed")
 endif()
diff --git a/cmake/onnxruntime_unittests.cmake b/cmake/onnxruntime_unittests.cmake
index 4b880c4437df..c0ea7892f2f2 100644
--- a/cmake/onnxruntime_unittests.cmake
+++ b/cmake/onnxruntime_unittests.cmake
@@ -1585,39 +1585,49 @@ if (NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
 
   if (NOT onnxruntime_ENABLE_TRAINING_TORCH_INTEROP)
     if (onnxruntime_BUILD_JAVA AND NOT onnxruntime_ENABLE_STATIC_ANALYSIS)
-        message(STATUS "Running Java tests")
+      block()
+        message(STATUS "Enabling Java tests")
+
         # native-test is added to resources so custom_op_lib can be loaded
-        # and we want to symlink it there
+        # and we want to copy it there
         set(JAVA_NATIVE_TEST_DIR ${JAVA_OUTPUT_DIR}/native-test)
         file(MAKE_DIRECTORY ${JAVA_NATIVE_TEST_DIR})
 
+        set(CUSTOM_OP_LIBRARY_DST_FILE_NAME
+            $<IF:${WIN32},$<TARGET_FILE_NAME:custom_op_library>,$<TARGET_LINKER_FILE_NAME:custom_op_library>>)
+
+        add_custom_command(TARGET custom_op_library POST_BUILD
+            COMMAND ${CMAKE_COMMAND} -E copy_if_different
+                $<TARGET_FILE:custom_op_library>
+                ${JAVA_NATIVE_TEST_DIR}/${CUSTOM_OP_LIBRARY_DST_FILE_NAME})
+
         # delegate to gradle's test runner
-        if(WIN32)
-          add_custom_command(TARGET custom_op_library POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different $<TARGET_FILE:custom_op_library>
-                          ${JAVA_NATIVE_TEST_DIR}/$<TARGET_FILE_NAME:custom_op_library>)
-          # On windows ctest requires a test to be an .exe(.com) file
-          # With gradle wrapper we get gradlew.bat. We delegate execution to a separate .cmake file
-          # That can handle both .exe and .bat
-          add_test(NAME onnxruntime4j_test COMMAND ${CMAKE_COMMAND}
-            -DGRADLE_EXECUTABLE=${GRADLE_EXECUTABLE}
-            -DBIN_DIR=${CMAKE_CURRENT_BINARY_DIR}
-            -DREPO_ROOT=${REPO_ROOT}
-            ${ORT_PROVIDER_FLAGS}
-            -P ${CMAKE_CURRENT_SOURCE_DIR}/onnxruntime_java_unittests.cmake)
-        else()
-          add_custom_command(TARGET custom_op_library POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different $<TARGET_FILE:custom_op_library>
-                          ${JAVA_NATIVE_TEST_DIR}/$<TARGET_LINKER_FILE_NAME:custom_op_library>)
-          if (onnxruntime_ENABLE_TRAINING_APIS)
-            message(STATUS "Running Java inference and training tests")
-            add_test(NAME onnxruntime4j_test COMMAND ${GRADLE_EXECUTABLE} cmakeCheck -DcmakeBuildDir=${CMAKE_CURRENT_BINARY_DIR} ${ORT_PROVIDER_FLAGS} -DENABLE_TRAINING_APIS=1
-                          WORKING_DIRECTORY ${REPO_ROOT}/java)
-          else()
-            message(STATUS "Running Java inference tests only")
-            add_test(NAME onnxruntime4j_test COMMAND ${GRADLE_EXECUTABLE} cmakeCheck -DcmakeBuildDir=${CMAKE_CURRENT_BINARY_DIR} ${ORT_PROVIDER_FLAGS}
-                          WORKING_DIRECTORY ${REPO_ROOT}/java)
-          endif()
+
+        # On Windows, ctest requires a test to be an .exe(.com) file. With gradle wrapper, we get gradlew.bat.
+        # To work around this, we delegate gradle execution to a separate .cmake file that can be run with cmake.
+        # For simplicity, we use this setup for all supported platforms and not just Windows.
+
+        # Note: Here we rely on the values in ORT_PROVIDER_FLAGS to be of the format "-Doption=value".
+        # This happens to also match the gradle command line option for specifying system properties.
+        set(GRADLE_SYSTEM_PROPERTY_DEFINITIONS ${ORT_PROVIDER_FLAGS})
+
+        if(onnxruntime_ENABLE_TRAINING_APIS)
+          message(STATUS "Enabling Java tests for training APIs")
+
+          list(APPEND GRADLE_SYSTEM_PROPERTY_DEFINITIONS "-DENABLE_TRAINING_APIS=1")
         endif()
+
+        add_test(NAME onnxruntime4j_test COMMAND
+            ${CMAKE_COMMAND}
+                -DGRADLE_EXECUTABLE=${GRADLE_EXECUTABLE}
+                -DBIN_DIR=${CMAKE_CURRENT_BINARY_DIR}
+                -DREPO_ROOT=${REPO_ROOT}
+                # Note: Quotes are important here to pass a list of values as a single property.
+                "-DGRADLE_SYSTEM_PROPERTY_DEFINITIONS=${GRADLE_SYSTEM_PROPERTY_DEFINITIONS}"
+                -P ${CMAKE_CURRENT_SOURCE_DIR}/onnxruntime_java_unittests.cmake)
+
         set_property(TEST onnxruntime4j_test APPEND PROPERTY DEPENDS onnxruntime4j_jni)
+      endblock()
     endif()
   endif()
 
diff --git a/java/build.gradle b/java/build.gradle
index 8b4d5429b0f7..34ac93cce6f4 100644
--- a/java/build.gradle
+++ b/java/build.gradle
@@ -199,7 +199,19 @@ test {
 	if (cmakeBuildDir != null) {
 		workingDir cmakeBuildDir
 	}
-	systemProperties System.getProperties().subMap(['USE_CUDA', 'USE_ROCM', 'USE_TENSORRT', 'USE_DNNL', 'USE_OPENVINO', 'USE_COREML', 'USE_DML', 'JAVA_FULL_TEST', 'ENABLE_TRAINING_APIS'])
+	systemProperties System.getProperties().subMap([
+		'ENABLE_TRAINING_APIS',
+		'JAVA_FULL_TEST',
+		'USE_COREML',
+		'USE_CUDA',
+		'USE_DML',
+		'USE_DNNL',
+		'USE_OPENVINO',
+		'USE_ROCM',
+		'USE_TENSORRT',
+		'USE_QNN',
+		'USE_XNNPACK',
+		])
 	testLogging {
 		events "passed", "skipped", "failed"
 		showStandardStreams = true