diff --git a/js/web/lib/wasm/jsep/webgpu/ops/3rd-party/matmul_packed_webgpu.ts b/js/web/lib/wasm/jsep/webgpu/ops/3rd-party/matmul_packed_webgpu.ts
index fee872f4120e3..52bb490f454ea 100644
--- a/js/web/lib/wasm/jsep/webgpu/ops/3rd-party/matmul_packed_webgpu.ts
+++ b/js/web/lib/wasm/jsep/webgpu/ops/3rd-party/matmul_packed_webgpu.ts
@@ -358,7 +358,7 @@ const matMulReadWriteFnSource =
           resStr += `\naIndices[${i}] = 0;`;
         });
         resStr += `\naIndices[${aRank - 2}] = u32(row);
-                   aIndices[${aRank - 1}] = u32(colIn);`;
+                   aIndices[${aRank - 1}] = u32(col);`;
         return resStr;
       };
       const getBIndices = () => {
@@ -372,7 +372,7 @@ const matMulReadWriteFnSource =
           resStr += `\nbIndices[${i}] = 0;`;
         });
         resStr += `\nbIndices[${bRank - 2}] = u32(row);
-                   bIndices[${bRank - 1}] = u32(colIn);`;
+                   bIndices[${bRank - 1}] = u32(col);`;
         return resStr;
       };
       const source = `
@@ -383,7 +383,8 @@ const matMulReadWriteFnSource =
       if(row < dimAOuter && col < dimInner)
       {
         ${getAIndices()}
-        value = ${aVariable.getByIndices('aIndices')};
+        // TODO: recover to use getByIndices/setByIndices when dxc is supported.
+        value = a[${aVariable.indicesToOffset('aIndices')}${component === 1 ? '' : `/ ${component}`}];
       }
       return value;
     }
@@ -395,7 +396,7 @@ const matMulReadWriteFnSource =
       if(row < dimInner && col < dimBOuter)
       {
         ${getBIndices()}
-        value = ${bVariable.getByIndices('bIndices')};
+        value = b[${bVariable.indicesToOffset('bIndices')}${component === 1 ? '' : `/ ${component}`}];
       }
       return value;
     }
@@ -404,10 +405,11 @@ const matMulReadWriteFnSource =
       let col = colIn * ${component};
       if (row < dimAOuter && col < dimBOuter) {
         var value = valueIn;
-        let coords = vec3<i32>(batch, row, colIn);
+        let coords = vec3<i32>(batch, row, col);
         ${hasBias ? 'value = value + bias[colIn];' : ''}
         ${applyActivation}
-        ${outputVariable.setByIndices('vec3<u32>(coords)', 'value')}
+        result[${outputVariable.indicesToOffset('vec3<u32>(coords)')}${
+          component === 1 ? '' : `/ ${component}`}] = value;
       }
     }
     `;
@@ -446,10 +448,9 @@ export const createMatmulProgramInfo =
       ];
 
       const components = isVec4 ? 4 : 1;
-      const A = inputVariable('a', inputs[0].dataType, [...outerDimsA, dimAOuter, dimInner / components], components);
-      const B = inputVariable('b', inputs[1].dataType, [...outerDimsB, dimInner, dimBOuter / components], components);
-      const output =
-          outputVariable('result', inputs[0].dataType, [batchSize, dimAOuter, dimBOuter / components], components);
+      const A = inputVariable('a', inputs[0].dataType, [...outerDimsA, dimAOuter, dimInner], components);
+      const B = inputVariable('b', inputs[1].dataType, [...outerDimsB, dimInner, dimBOuter], components);
+      const output = outputVariable('result', inputs[0].dataType, [batchSize, dimAOuter, dimBOuter], components);
       variables.push(A);
       variables.push(B);
       variables.push(output);
@@ -457,7 +458,7 @@ export const createMatmulProgramInfo =
       const hasBias = inputs.length > 2;
       const declareFunctions = matMulReadWriteFnSource(component, hasBias, applyActivation, variables);
       if (hasBias) {
-        inputVariables.push(inputVariable('bias', inputs[2].dataType, [dimBOuter / components], components));
+        inputVariables.push(inputVariable('bias', inputs[2].dataType, [dimBOuter], components));
       }
       const getShaderSource = (shaderHelper: ShaderHelper) => `
   const dimAOuter: i32 = ${dimAOuter};