(CNN) -- Police alternately closed and reopened commuter train stations in downtown San Francisco Monday after demonstrators gathered to protest recent shootings by the train system's police officers.

Police in helmets and protective gear shut the Civic Center station about 45 minutes after the demonstration began at 5 p.m., making protesters and media crews head for the exits. Soon after, officials also closed the Powell Street BART station but that station was reopened less than an hour later.

The Bay Area Rapid Transit system reported on its Twitter page that all stations were open less than an hour and a half after the demonstration began at the Civic Center station. Then, the Powell Street station was closed again for a time, only to be reopened with the Civic Center station being closed again.

And so it went.

At least three protesters -- two men and a women -- were taken into custody during the protest at the the Civic Center, after they engaged in verbal confrontations with police.

One of the men, who spoke to the demonstrators with a litany of complaints against BART police, was taken from the platform in handcuffs by officers as demonstrators shouted, "Let him go, let him go."

Meanwhile, trains continued to run amid the protest.

After the Civic Center station was closed, demonstrators accompanied by a line of police officers began a march on city streets.

BART officials had said that they planned to beef up security at the Civic Center station because of the protest.

"BART may need to close some stations temporarily or make other service adjustments on short notice," train officials said in a statement before the protest.

BART has been at the center of controversy about shootings by its officers, the latest being last month that resulted in the death of Charles Hill, 45.

Last week, hackers attacked BART's website and posted the home addresses and other information of all 102 police officers on the train system's police force.

There also have been several other attempts at protests, including one earlier this month that BART officials quelled by cutting cell phone signals at some subway stations.

The train system's board members have scheduled a special meeting for Wednesday to discuss that controversial decision.

The decision to cut cell phone service elicited criticism from civil liberty organizations, the San Francisco Chronicle's editorial page and others.

CNN's Divina Mims contributed to this report