"Our hearts go out to their families," Health Commissioner Thomas Frieden said.
The outbreak began more than a month ago when hundreds of students at St. Francis Preparatory School in the Fresh Meadows section of Queens became sick.
All of the four known victims also had other underlying health conditions, Frieden said.
The two people whose deaths were disclosed Tuesday were a 41-year-old Queens woman and a 34-year-old Brooklyn man. Lab results confirmed that they had swine flu but the exact cause of their deaths will be determined by autopsies, Frieden said.
Meanwhile, the Queens school whose assistant principal became the first New Yorker to die of swine flu once again bustled with activity Tuesday.
The Susan B. Anthony Intermediate School, Intermediate School 238, was among 20 schools or programs that reopened after being shuttered as a precaution amid the city's 330 confirmed cases of the H1N1 virus.
"We just want to keep things moving," said principal Joseph Gates as he helped load two buses of students headed for a school trip to Washington, D.C.
Mitchell Wiener, I.S. 238's assistant principal, died May 17. A woman in her 50s died Saturday. The names of the swine flu victims other than Wiener have not been released.
At Public School 19 in the Corona neighborhood of Queens, Chancellor Joel Klein welcomed the children to their reopened school.
Third-grader Eric Sobarzo was dropped off by his big brother, Peter DeCaprio, who said he was confident that "whatever the problem was here, they must have fixed it."
Of the 20 schools or school programs that were to reopen Tuesday, 16 are in Queens, two in the Bronx and one each in Manhattan and Brooklyn.
Five others closed in early May had already reopened.
But as some schools reopened, five others closed Tuesday: one each in the Bronx, Queens, and Manhattan, and two in Brooklyn. They will reopen Monday.
City officials said last week the reason for the closings was mainly to protect the most vulnerable - young children, the elderly, pregnant women and anyone with a chronic medical condition like asthma or diabetes. Some schools reported last week that as many as two-thirds of their students were absent.
Frieden said his department surveyed two schools with high absentee rates and found that only one-fourth of the absent children were actually ill.
For facts about influenza, and more information about swine flu, please visit the Health Department and CDC websites. Some specific resources:
From New York City Health Department
Facts about flu
From Centers for Disease Control and Prevention
General information about swine flu
Swine Flu Case Definitions
Swine Flu Infection Control and Patient Care
Preventing the Flu
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