The U.S. Customs and Border Protection Service told CBS News that an X-ray machine "revealed 'anomalies' in two containers from Pakistan."
Customs agents used the "gamma-ray" device at Terminal 18, south of downtown, to peer through the containers' steel walls and detected some items inside did not match the containers' manifest, agency spokesman Mike Milne said.
The containers were then subjected to the dogs, which raised concerns about explosives. A bomb squad that searched the containers found nothing dangerous.
Officials said the containers were supposed to contain oily rags, which are often shipped internationally for recycling or use in packaging. Authorities continued examining the cargo Wednesday afternoon.
It was not immediately clear why the dogs were mistaken.
Milne said the ship had originated in Hong Kong and made stops in China before arriving Monday in Seattle.
Terminal 18 covers nearly 200 acres, making it the port's largest container terminal and one of the largest in the nation. It serves more than 20 steamship lines and receives more than 40 vessels each month.