Early last month, a BART police officer shot and killed a knife-wielding homeless man at the San Francisco Civic Center station. The incident provoked a series of small protests that drew little attention until Aug. 11, when the transit agency took the unusual step of shutting down cellphone service for several hours as activists prepared for another rally.

With that flip of a switch, BART has come under siege — in cyberspace and underground.

According to officials, BART’s technology personnel have been working round the clock to fend off a disparate group of hackers who penetrated the agency’s Web sites last week and released sensitive information, in retaliation for the shutdown of the cellphone and wireless services.

The Federal Communications Commission is investigating the decision to shut down the services, and the American Civil Liberties Union is considering a lawsuit against BART on the ground of First Amendment violations.

The protests, while still small, appear to have grown in number and potency. Using the Twitter hashtag #MuBARTek, a wry reference to Hosni Mubarak’s efforts to shut down communications before he was toppled as president of Egypt, activists organized a new round of protests that forced BART to shut down four stations during rush hour last Monday.

Another rally is planned for this Monday. Protesters threatened that more would follow “until BART decides to back away from their policy of cellphone censorship,” according to one message from a person with the Twitter handle @OpBART.

Some BART board members, like Lynette Sweet, have criticized the decision to shut down cellphone service. “Rather than thwart protesters,” Sweet said, “we’ve invited in a whole new arena of people that we have to deal with now. It’s like relighting a fire that was already out.”

The episode has been a sobering lesson in how even an agency that carries some 350,000 passengers over 104 miles of track every workday can be brought low by a seemingly ragtag group of activists who identify themselves by pseudonyms like Lamaline_5mg.

According to David Wagner, a computer science professor at the University of California, Berkeley, the hackers were relatively unsophisticated and most resembled “bored rebellious teenagers.”

BART officials have labeled the protesters “cyberterrorists” and said the agency’s actions were necessary to preserve safety in an environment of fast-moving trains and electrified rails.

“You have the ability to limit people’s free speech when public safety is at risk,” said the BART board president, Bob Franklin, who announced Thursday that the board would hold discussions this week on its policy for shutting off cellular communications.

But Jean Hamilton, president of a union that represents 200 BART employees, said the agency’s leadership had mishandled the crisis. “We feel under fire, and we feel everything we’ve done to promote transit is in the toilet,” Hamilton said. “All people are talking about is freedom of speech and will the trains be stopped again tonight.”

The crisis began July 3 with a report to police dispatchers that a man in a tie-dyed T-shirt was walking the platform of the Civic Center station with an open bottle of alcohol. BART says the man, Charles Hill, approached officers with a four-inch-long knife and was preparing to throw it when an officer shot and killed him. The shooting is under investigation.

The incident caught the attention of the group No Justice No BART, which formed in response to the 2009 shooting of an unarmed man, Oscar Grant III, on the platform of the Fruitvale station in Oakland. The group has about 500 fans on Facebook. Its leader, a research scientist who calls himself Krystof, has clashed repeatedly with the BART board.

“He’s shown up at our meetings — he’s very cynical about BART,” Franklin said. “He wants to disband the BART police, and he’s very media savvy.”

Krystof countered in an interview that “BART has been really insular — they’re not used to outside scrutiny.”