"The coastguard is flying a plane to the area and a patrol ship is heading there too," a spokesman told AFP.
"But we haven't been able to confirm the safety of the seven members."
The capsized Japanese boat was found earlier in the day 410 kilometres southwest of Palau after the crew sent an SOS on Monday.
Nearby vessels including a ship from Japan's National Fisheries University joined the search and Japan had asked Guam for cooperation, the spokesman added.