Dr. Perea-Henze said he hoped to “accelerate” Outreach NYC over the next two years.

“I believe there is progress being made,” said Dr. Perea-Henze, who dealt with veteran homelessness, mental illness and drug addiction when he served as the assistant secretary for policy and planning in the United States Department of Veterans Affairs during the Obama administration. “But frankly, for the next two years, I will be responsible for making sure that progress accelerates.”

Dr. Perea-Henze has a master’s degree in public health from Yale University and was the first openly gay Latino to be sworn in as a sub-cabinet secretary. A Mexican immigrant, he speaks four languages and started his career at the New York City Health and Hospitals Corporation, where he developed the division of infectious diseases during the AIDS epidemic. His first partner died from AIDS.

Dr. Perea-Henze is replacing Dr. Herminia Palacio, who resigned in June to become the president and chief executive of the Guttmacher Institute. He takes over an agency charged with overseeing public health, with a particular focus on helping the most vulnerable New Yorkers.

He begins his tenure amid calls to set aside and build more housing specifically for the homeless as part of the mayor’s affordable housing plan. The city has so far struggled to keep pace with Mr. de Blasio’s plan to build 90 new homeless shelters, with many meeting opposition from neighborhood residents.

Although the number of people in shelters has been flat for the first time in a while, Dr. Perea-Henze said “we still need to turn the tide” on the issue.

“Coming in to tackle homelessness is probably the best thing that I can do to help New Yorkers,” he said. Asking city employees to be trained to identify and help the homeless is a natural progression, he said.

Giselle Routhier, policy director of the Coalition for the Homeless, an advocacy group, said the city’s focus on this new effort was “frustrating” because “the problem with street homelessness is not a lack of outreach workers, the problem is they are not being offered something meaningful like housing or a low-barrier shelter.”