Gary Jenkins was being investigated after allegedly covering up crowded conditions at shelters where migrants were being housed.
He made the announcement that he would resign Tuesday night.
"I'm really proud and privileged to serve under Mayor Eric Adams. He's is a phenomenal leader, a caring person, but just, just the epitome of a professional. So no, there's no discord. There's no running away. This was something that was already planned," Jenkins said.
Meanwhile, a sixth migrant shelter will be opening at the Holiday Inn in the Financial District of Manhattan.
The hotel filed for bankruptcy in November.
The city will pay the hotel's owner $190 a room per night.
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