Gary Jenkins was being investigated after allegedly covering up crowded conditions at shelters where migrants were being housed.
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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.
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The city will pay the hotel's owner $190 a room per night.
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