Mayor Bill de Blasio on Tuesday appointed a new deputy mayor to help oversee his administration’s response to the city’s homelessness crisis.

Dr. Herminia Palacio, a Bronx-born epidemiology specialist and director of the philanthropic Robert Wood Johnson Foundation, will manage eight city agencies, including the Department of Homeless Services, de Blasio said at a City Hall news conference.

She succeeds Lilliam Barrios-Paoli as the deputy mayor for health and human services. Barrios-Paoli resigned in late August as the city was facing increasing concerns over its homeless population.

De Blasio’s commissioner for homeless services, Gilbert Taylor, left in mid-December and has not been replaced.

Meanwhile, nearly 100 homeless people were taken off city streets overnight by NYPD and city outreach workers as temperatures fell far below the freezing point, according to de Blasio’s office Tuesday.

Of the 97 individuals taken to shelters and other indoor locations, at least 12 voluntarily went to a hospital and one person was transported involuntarily for a mental health evaluation, according to the tally taken between 8 p.m. and 8 a.m.

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The actions took place as an executive order by Gov. Andrew M. Cuomo took effect, mandating that authorities across the state move people out of the cold when the mercury dips below 32 degrees.

But de Blasio — who has feuded with his fellow Democrat over management of the city’s homelessness crisis — indicated that the state edict didn’t change the way the city conducted its work.

“As in previous years, city outreach teams scoured neighborhoods throughout the five boroughs last night to help bring New Yorkers out of the cold,” the mayor said in a statement.

Cuomo, meanwhile, honed his attacks on the state of the city’s shelter system. He emphasized that some homeless people preferred frigid cold streets over “disgusting” shelters.

“What you have more and more in New York City is people say, ‘I’m not going to the shelter system. It’s dangerous. It’s dirty,’ ” the governor said at an unrelated Woodbury event on Tuesday morning. “So the outreach fails because of the shelter system.”

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He said it was “undeniable” that the city’s homelessness crisis is worsening. Cuomo also contradicted de Blasio’s frequent argument that economic factors have contributed to homelessness in the city.

“The homeless problem, primarily in New York City, is getting worse,” Cuomo said. “The homeless problem is not an economic problem, it’s not a complicated problem, it’s a human problem.”

De Blasio acknowledged at City Hall that there is “more work” to be done in improving city shelters, but said many are run well.

In Nassau County, the total number of individuals in emergency housing was 918, according to county spokesman Brian Nevin. Two people were removed to hospitals as a result of canvasses during the night, he said.

In Suffolk County, Department of Social Services provided shelter to 60 additional homeless people overnight, on par with past years’ initial blast of cold weather, the agency’s commissioner John O’Neill said.

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“It’s the normal expected increase when we see the first cold snap of the year,” he said.

As of Tuesday afternoon, he did not know of any undocumented immigrants being served in shelters, who before Cuomo’s order had been unable to get county assistance. He was also unaware of any police transportation of mentally ill people who refused shelter.

With Robert Brodsky, David M. Schwartz and James T. Madore