It was a commuter nightmare on the rails Tuesday morning.

Service on the B line was briefly suspended in both directions after a train’s brakes were automatically activated at the Prospect Park station in Brooklyn and officials investigated a smoke issue there, the MTA said.

By 8:50 a.m., B and Q train service resumed with delays after the MTA “addressed a source of smoke at Prospect Park,” the authority posted on its website.

The FDNY received a call for an odor of smoke in the station at 7:19 a.m. Firefighters responded and closed out the call within 10 minutes, FDNY officials said.

The MTA initially tweeted from its @NYCTSubway account just before 7:30 a.m. that the delays were caused because a train’s brakes were automatically activated.

“I was on this train, at first the train operator said it was the transformer. THIS WAS NOT AN EMERGENCY BRAKE SITUATION! MTA needs to stop lying to commuters, kills your already low credibility. We were stuck for 1/2 hour, no air, like animals!” Twitter user @GilliannW tweeted in response.

@NYCTSubway tweeted back: “Hi Gilliann, the brakes were automatically activated, there was a loud noise, and smoke began to issue. We are currently investigating what’s going on and can’t say definitively at this time. Hope your day goes up from here.”

Meanwhile, as of 8:29 a.m., southbound 6 trains were running with delays because of signal problems at Brooklyn Bridge-City Hall and northbound 1 trains were operating with delays due to the same issue at the 181st Street station.

“You may experience minor delays in southbound 4 and 5 train service,” the MTA warned straphangers.

Also, 7 trains were running with delays in both directions after an “unauthorized person” was removed from the tracks at the Vernon Boulevard-Jackson Avenue station in Queens, the MTA said.

Additional reporting by Stephanie Pagones