Include the following permissions in your manifest
<uses-permission android:name="android.permission.READ_CALL_LOG"/>
<uses-permission android:name="android.permission.WRITE_CALL_LOG"/>
Try the following code
getContentResolver().delete(CallLog.CONTENT_URI , "type="+CallLog.Calls.MISSED_TYPE , null);
Based on http://developer.android.com/reference/android/provider/CallLog.Calls.html#TYPE