The feds have opened a criminal investigation into New York City’s migrant hotels — demanding Wednesday that staff turn over names of “aliens” housed at shelters, The Post has learned.

The Justice Department is investigating funding and operations at two Manhattan hotels being used as migrant shelters, according to several reports.

Prosecutors asked for a list of names of “aliens” living at a Manhattan hotel. The city houses about 43,000 migrants in shelters, including dozens of converted hotels.