MUNI announced on Monday that, though they were hacked, it was on internal servers and did not affect the safety of riders.
"You Hacked, ALL Data Encrypted,” a message appearing on the transportation network’s computers read on Friday evening.
The hackers reportedly demanded 100 Bitcoins (about $73,000) to end the attack. It is not currently known if the agency paid the ransom.
As ticketing systems were disrupted, people traveling between the city's underground stops were able to ride free throughout the holiday weekend.
“The fare gates were closed on Friday and Saturday as a precaution, to minimize any impact to our customers. They were operational again on Sunday,” Muni spokesman Paul Rose told USA Today.
The transit agency’s website now states that, “the situation is now contained and we have prioritized restoring our systems to be fully operational.
"Encrypting files and asking for ransom has been a popular method of attack in recent years. Earlier this year, the Melrose Massachusetts Police department actually paid the ransom to unlock their files,” Tim Erlin, senior director of IT security and risk strategy for the security firm Tripwire, told USA Today.