The Metropolitan Transportation Authority (MTA) says the trains "bumped into each other" this morning but didn't derail.
The agency says one MTA worker is being treated for non- life-threatening injuries.
There were no passengers on the trains, and MTA officials say the accident is having no impact on subway service during the morning commute.
Fire department officials say firefighters removed one person from the Manhattan side of a tunnel under the East River after the accident occurred around 5:10 am (local time).
Media outlets report that the trains collided in the 53rd Street tunnel that carries passenger trains between Manhattan and Queens. That stretch of tunnel has been undergoing repairs.
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