The 4,143-tonne New Lucky VII, which was carrying lumber from Papua New Guinea to China, disappeared on Tuesday.
The vessel's last known location was about 100 kilometres (60 miles) off the southern Japanese island of Amami Oshima, officials said.
"Hong Kong maritime rescue authorities asked us to check the situation of the ship as contact with it has been lost," said an official at the 10th Regional Coast Guard Headquarters.
"We spotted oil floating in wide areas... (but) we haven't found the ship yet," the Japanese official added.
The ship had 17 crew members - 14 Indonesians, two Chinese and one Taiwanese - on board, the coastguard said, citing information from Hong Kong authorities.
The coastguard added that two boats and another two planes had been sent out to search for the vessel.
Japan was hammered by a huge storm earlier this week with violent winds and rain that caused transport chaos and left at least five people dead.