An aerial inspection suggested that there was no one on board, Transport Canada spokeswoman Sau Sau Liu told AFP.
The 65-meter (210-foot) vessel was spotted Tuesday by a Canadian Forces aircraft on a routine surveillance patrol, and its Japanese owner has been notified, said Transport Canada.
A military photo shows the ship, streaked with rust but intact, floating 278 kilometers (150 nautical miles) off the southern coast of Haida Gwaii islands, some 1,500 kilometers (930 miles) north of Vancouver.
"The vessel is considered an obstruction to navigation," Transport Canada said in a statement, adding that it was being monitored for pollution.
The ship is the first, and largest, item confirmed to have crossed the Pacific Ocean to North America from Japan's devastating earthquake and tsunami on March 11, 2011.
Near Midway Atoll in the deep Pacific, a Russian ship spotted an intact 20-foot Japanese boat from Fukushima last fall, along with debris such as a television and other household appliances, the University of Hawaii said.
Ocean researchers based in Hawaii are monitoring the debris from the tsunami, which they earlier predicted would reach western North America early next year.
There have been reports of Japanese bottles and other items washing ashore, but it's not clear if they were from the tsunami.
Earlier this month, Canada's western province of British Columbia and the western US states of Washington, Oregon and California signed an agreement to coordinate management of the tsunami debris when it reaches shore, and to return items of sentimental value to Japan.
The Japanese fishing boat that was found this week is not expected to reach landfall for another 50 days, said a media statement by Washington Senator Maria Cantwell, who has a special interest in marine issues.