diff --git a/onnxruntime/contrib_ops/webgpu/bert/rotary_embedding.cc b/onnxruntime/contrib_ops/webgpu/bert/rotary_embedding.cc
index 20e1583e0da8f..b33084d60cec3 100644
--- a/onnxruntime/contrib_ops/webgpu/bert/rotary_embedding.cc
+++ b/onnxruntime/contrib_ops/webgpu/bert/rotary_embedding.cc
@@ -27,7 +27,7 @@ Status RotaryEmbeddingProgram::GenerateShaderCode(ShaderHelper& shader) const {
   const auto& sin_cache = shader.AddInput("sin_cache", ShaderUsage::UseUniform);
   const auto& output = shader.AddOutput("output", ShaderUsage::UseUniform);
   // TODO: remove output_indices.
-  const auto& output_indices = shader.AddIndices("output_indices", false);
+  const auto& output_indices = shader.AddIndices("output_indices", ShaderUsage::None);
   const auto interleaved_str = interleaved_ ? "true" : "false";
   shader.MainFunctionBody() << "  let half_rotary_emb_dim = uniforms.cos_cache_shape[1];\n"
                                "  let bsnh = global_idx / uniforms.global_stride % uniforms.global_shape;\n"
diff --git a/onnxruntime/core/providers/webgpu/shader_helper.cc b/onnxruntime/core/providers/webgpu/shader_helper.cc
index 19cab9b178b1f..db14cb88d1963 100644
--- a/onnxruntime/core/providers/webgpu/shader_helper.cc
+++ b/onnxruntime/core/providers/webgpu/shader_helper.cc
@@ -104,12 +104,19 @@ const ShaderVariableHelper& ShaderHelper::AddOutput(const std::string& name, Sha
   return AddVariableImpl(false, name, usage, dims);
 }
 
-const ShaderIndicesHelper& ShaderHelper::AddIndices(const std::string& name, bool use_uniform) {
+const ShaderIndicesHelper& ShaderHelper::AddIndices(const std::string& name, ShaderUsage usage) {
   const size_t indices_index = indices_vars_.size();
+  ORT_ENFORCE(indices_index < program_.Indices().size(),
+              "Too many indices in the program (", program_.Indices().size(), ")");
+
+  // usage of indices should not use flag other than UseUniform and UseIndicesTypeAlias
+  ORT_ENFORCE(!(usage & ~(ShaderUsage::UseUniform | ShaderUsage::UseIndicesTypeAlias)),
+              "Invalid usage for indices variable ", name);
+
   return *indices_vars_.emplace_back(
       std::make_unique<ShaderIndicesHelper>(name,
                                             ProgramVariableDataType::InvalidType,
-                                            use_uniform ? ShaderUsage::UseUniform : ShaderUsage::None,
+                                            usage,
                                             program_.Indices()[indices_index]));
 }
 
diff --git a/onnxruntime/core/providers/webgpu/shader_helper.h b/onnxruntime/core/providers/webgpu/shader_helper.h
index 64b4c054f93d4..e5f316a46bedc 100644
--- a/onnxruntime/core/providers/webgpu/shader_helper.h
+++ b/onnxruntime/core/providers/webgpu/shader_helper.h
@@ -86,7 +86,7 @@ class ShaderHelper final {
                                         ShaderUsage usage = ShaderUsage::UseIndicesTypeAlias | ShaderUsage::UseValueTypeAlias | ShaderUsage::UseUniform);
 
   // Add an indices variable to the shader.
-  const ShaderIndicesHelper& AddIndices(const std::string& name, bool use_uniform = true);
+  const ShaderIndicesHelper& AddIndices(const std::string& name, ShaderUsage usage = ShaderUsage::UseUniform);
 
   // Get the string stream for additional implementation code to the shader.
   inline OStringStream& AdditionalImplementation() {