The alert was issued to US citizens yesterday.
An embassy spokesperson today said there is nothing linking the warning with AirAsia Flight 8501. The plane crashed into the Java Sea a week ago after taking off from Surabaya, killing all 162 passengers and crew on board.
The US Navy is taking part in an international effort to recover bodies and locate the wreckage.
Indonesia's national police spokesman Brig. Gen. Agus Riyanto says he's unaware of any terrorism threat against banks and hotels in Surabaya but added that security would be increased.