The International Longshore and Warehouse Union said about 10,000 workers joined the anti-war protest, in part because, the union argues, that big shipping companies are profiting from the war.
The protest also takes place on the same day that George Bush, the US president, declared major combat operations in Iraq to be over five years ago.
However, port officials cast doubts over the war as the reason for the protest.
Getzug said the action came two months prior to the expiration of an agreement on working conditions between the ports and workers.
"Today's actions raised the question of whether this was an attempt to leverage contract negotiations," he said in a statement.
Paul Bingham, an economist with the Global Insight group, which tracks container volume and congestion at US ports, said shippers and carriers were prepared for the stoppage.
"If this had come as a surprise it would have been a lot more serious in its impact," said Bingham, also noting that it was not peak season for shipping.