No equipment moved out of the port Wednesday, and a handful of people stood outside the port's main gate late Wednesday night.
Dick Machlan, the Olympia Police Department's administrative services manager, told reporters earlier in the day that protesters had been overly aggressive.
A small group of protesters threw rocks and rolled trash bins or threw debris onto roads Tuesday night to stop the convoys of Stryker vehicles, accompanied by patrol cars, after the convoys left the port through a secondary exit.
Windows at U.S. Bank's downtown branch were broken, and rocks thrown by a small group of protesters hit one officer in the knee and broke windows on a patrol car, Olympia police Lt. Jim Costa said Tuesday night.
Earlier Tuesday, port maintenance workers had found concrete on the railroad leading out of the property and removed it. Railcars carrying military equipment and vehicles moved from the port to Fort Lewis on Wednesday morning.
"We're monitoring for any other possible incidents," said Patti Grant, port spokeswoman.
Olympia police are accustomed to dealing with protests, but this group "moved it to a different realm," Machlan said.
"Some people are there to make a point about the war," he added. "But once the point has been made, they need to move on."
No one who was arrested was thought to have damaged property, Machlan said.
Protesters said it was police who escalated the situation, shifting from individually arresting protesters who blocked the port's main access road to using batons and pepper spray and dragging people to disrupt a nonviolent demonstration. Thirty-eight women and five men were arrested.
"Most of the people here are peaceful and would have submitted to being arrested without resisting," said Robert Whitlock, 29, one of the protesters who were arrested. He was at a vigil Wednesday evening at Percival Landing that drew more than 70 people.
Kim Chaplin, 35, was among the women who sat in the road in a show of solidarity when police began the individual arrests. She said the women told police repeatedly that they would not resist arrest. Halfway through, officers began aggressively moving back the supporters standing behind them in an attempt to disperse the crowd to avoid making more arrests, she said.
"It was like they were trying to predict what was going to happen next and contain the situation, in an escalating way," said Chaplin, who said she was in police custody from about 10:30 p.m. Tuesday to 4 a.m. Wednesday.
Police Chief Gary Michel suggested the change in tactics was because the department didn't have space to hold dozens of people after their arrests. The Olympia City Jail has room for 28 people. All the protesters police arrested had been booked and were released by Wednesday morning.
"We were totally full," he said.
City attorneys will review the cases and decide whether to prosecute the protesters, most likely for pedestrian interference, a misdemeanor. It is illegal to obstruct traffic on a public roadway.
Demonstrators have claimed police have used excessive force since shortly after their protests began Nov. 6, the day after the USNS Brittin docked at the Port of Olympia to unload equipment and vehicles used by the 3rd Stryker Brigade Combat Team, 2nd Infantry Division during 15 months in Iraq. The brigade's 3,600 soldiers returned home last month.
Olympia Port Militarization Resistance has coordinated the protests to oppose the military's use of the publicly funded port and to demand an immediate withdrawal of U.S. forces from Iraq. Its members planned to "contain" the equipment and vehicles at the port to stop them from being used in Iraq again, but the police presence has thwarted those efforts.
The department has received one formal complaint of excessive force, and it is being investigated, Olympia police Lt. Bill Wilson said.
"I had been expecting more based on what I had heard and read," he said.
Most of the equipment and vehicles have returned to Fort Lewis, but some remains at the port, Olympia police Cmdr. Tor Bjornstad said.
Michel wouldn't guess Wednesday how much the overtime and extra resources that the Olympia police used during the protests will cost.
"We're probably a week away from knowing that exactly," he said.
Fifty-eight protesters have been arrested during the recent protests. Thirty-seven were arrested in May 2006 when the brigade's equipment was loaded at the Port of Olympia on its way to Iraq.
Olympian reporter Jeremy Pawloski contributed to this report.