Riders, be ready: The NYPD can commandeer your bus at any time to take prisoners to jail cells.

Today, MTA Chairman Joseph Lhota backed the NYPD’s controversial confiscation of a public bus to transport Occupy Wall Street protesters who were arrested at Zuccotti Park on March 17th, the sixth-month anniversary of the movement.

“When you have situations like this and the police determine that they need to get from point A to point B, we will help them,” Lhota said.

Protesters said police officers stopped an M5 bus, which runs the length of Manhattan from South Ferry to the George Washington Bridge, around midnight by Zuccotti Park. They said the NYPD made the paying passengers get off and in their place, boarded dozens of arrestees and re-routed the vehicle to the Midtown South police precinct.

It is unclear whether those passengers who were kicked off were reimbursed for their fare.

Drivers who object to working with police can opt out of driving prisoners, Lhota said, because the Police Department has officers trained to drive buses. Lhota said the MTA often works with other city agencies to transport people in emergencies like 9/11 and during Tropical Storm Irene.

“This relationship between the transit authority and the NYPD goes back to as long as the transit authority has been around,” said Lhota.

But Occupy Wall Street protesters stormed today’s board meeting, to voice their anger over the practice.

“Public resources have been commandeered by a private army,” said Shawn Carrie, 22, an Occupy Wall Street protester who was arrested on March 17th, referencing when Mayor Michael Bloomberg infamously declared on Nov. 29th, “I have my own army in the NYPD.”

OWS chains open subway entrances

Occupy Wall Street protesters chained open more than 20 stations across the city this morning for free entry.

The gates were open at about 5 a.m., and the MTA cut most of them down by 8:30 a.m.

They said it was in response to “escalating service cuts, fare hikes, racist policing, assaults on transit workers’ working conditions and livelihoods.”

Protesters said they worked in conjunction with “rank and file” workers from the Transport Workers Union Local 100 and the Amalgamated Transit Union, but neither union has returned Metro’s request for comment or condemnation.

For more local news, follow Emily Anne Epstein on Twitter @EmilyAEpstein.