The Long Island Rail Road train crashed around 8:30am (1330 GMT) at Atlantic Terminal in the heart of the New York borough.
"76 non life-threatening injuries reported at scene of LIRR train derailment, Atlantic Terminal Brooklyn," the New York Fire Department said in a tweet.
103 injuries reported at scene of Atlantic Terminal LIRR train derailment, all non-life-threatening pic.twitter.com/t5p78cAFlU
— FDNY (@FDNY) January 4, 2017
Passengers rushed out as smoke filled the tunnel. The impact bent the train's doors and smashed windows.
Some of the injured were brought out on stretchers.
Commuter Aaron Neufeld said on Twitter that the crash was "crazy", but added, "Seems only a few people are lightly injured."
New York's emergency notification system warned of traffic and transit delays and road closures in the area.
In September, a train derailed during rush hour as it entered the station in Hoboken, New Jersey, near New York. One person died and 114 were injured.
An investigation into that incident, in which the train entered the station at unusually high speed, is ongoing.
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