Trains were rolling Monday night on the B and Q lines, but the delays continued into the evening.
Service had to be shut down during rush hour after chunks of cement tumbled onto the railbed from the ceiling above.
It happened at about 1 p.m. on the express track near the DeKalb Avenue station in Fort Greene.
As work crews struggled to clear the tracks, the delays rippled through Fort Greene, Downtown Brooklyn, and beyond.
"I was on a D train heading into Brooklyn from 34th and what normally takes 45 minutes took twice as long, sat on the (Manhattan) bridge about 25 minutes," said commuter Tavie Rhymes.
Nothing like a two hour commute home on a crowded subway train! Thanks, "falling debris at DeKalb"! ?— tavie rhymes w/gravy (@TheRealTavie) June 6, 2016
"Hopelessly trapped," wrote another woman.
Hopelessly trapped on @NYCTSubway - falling debris at Dekalb stop? 55 min and counting from Broadway Lafayette to Brooklyn— Cybele Raver (@ccybeleraver) June 6, 2016
It comes one year after an audit by the City Comptroller revealed a shocking lack of basic cleanliness and maintenance in many subway stations.
There was no train on the tracks at the time of the incident.
Crews worked into the evening to clear the debris that fell onto the roadbed of the B & Q lines.
The MTA reported delays in both directions on the B, D, N, Q and R subway lines.