The former Bishop Ford Catholic school opened 126 pre-K seats after holding a last-minute lottery.
Some pre-K programs in Fort Greene and Clinton Hill are in high demand while others have empty seats.
The city has closed Rainbow Montessori's pre-k programs in The Bronx.
At least one parent said he was not informed that a Hudson Heights pre-K would not open Thursday.
Tens of thousands of 4-year-olds started school Thursday in new full-day pre-K seats.
The Department of Investigation says it is investigating at least 5 of the 9 shuttered pre-K programs.
Education workers with no inspection experience were given crash course on pre-K walk-throughs.
Officials abruptly canceled 9 pre-K programs and postponed 36 more just before the first day of school.
The mayor said the comptroller's report misrepresented the current status of pre-K expansion.
Comptroller Scott Stringer said he would not be able to review all the contracts before school starts.
The annex at the Garden School on Northern Boulevard is still being built out.
The full day pre-K classes are planned for locations in Woodhaven and Ravenswood in Astoria.
The city wants 53,000 "full day" pre-K seats in September, but a six-hour day is hard on some families.
A new bill that would alarm elementary school exits is crucial with universal pre-K, its sponsor says.
More than 200 pre-K seats will be added to District 2 schools, but none are on the Upper East Side.
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