Bomb-sniffing dogs indicated that two containers from Pakistan could contain explosives.
Officials are still trying to determine exactly what is in the containers. It was not immediately clear why the dogs were mistaken.
Dozens of personnel were evacuated from Terminal 18, south of downtown, and nearby businesses were advised to keep their workers indoors.
U.S. Customs and Border Protection agents used a "gamma-ray" device to peer through the containers' steel walls to determine what they contained, said spokesman Mike Milne. It detected some of the items did not appear to match what was listed on the containers' manifest, he added.
Officials said the containers were supposed to contain oily rags, which are often shipped internationally for recycling or use in packaging.
The Port of Seattle bomb squad used explosive charges to cut into the containers, which may have detonated any explosives therein, said spokesman Mick Shultz. Milne said the ship had originated in Hong Kong and made stops in China before arriving in Seattle on Monday.
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.
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