Mr. Moschitta said the problems stemmed from rusted sound attenuators in the ducts, which reduce mechanical equipment noise. “As the forced air goes through the ducts, little fragments break off,” he said.

“When you have a 45-year-old facility, things rust,” he added.

The report also noted the presence of spores of cladosporium, a common mold that can grow indoors on surfaces when moisture is present and can cause allergic reactions and respiratory problems.

Ronald Brattain, the chief of the hospital’s engineering service, said that the operating room air-supply ducts have been wet and regularly exposed to high humidity because they pull air from the outside, as is common in older V.A. hospitals. “The humidity that is in the air is drawn through the air handler, and so that by itself creates a moist environment,” he said.

The entire V.A. system has been plagued with crumbling buildings and deferred maintenance. According to the V.A., roughly 60 percent of its medical facilities are more than 50 years old. The department’s inspector general issued an audit report in 2014 warning that there was a $10 billion to $12 billion backlog in maintenance throughout the system, jeopardizing patient safety at a time when aging baby boomers and newly enrolled veterans of Iraq and Afghanistan increasingly sought care at V.A. hospitals.

Mr. Moschitta said that one backup plan under discussion at Northport was to bring in mobile surgical units that would be parked outside the emergency room on the lawn, but those units rent for $70,000 to $85,000 per month.

Mr. Moschitta said he is confident the problem will be solved with the installation of high efficiency particulate air filters in each of the vents in the operating rooms, and that at least one of the surgical suites will be up and running in the near future. “Barring any mishap, we’re ready to go on June 1,” he said. “A lot of these facilities are vintage.”

It is not only the operating rooms that have been affected at Northport. In the basement of Building 200, one floor down from the operating rooms, the air-conditioning broke down in March 2015, and since then particulates have accumulated in five ultrasound rooms and an M.R.I. area. Mr. Brattain said the problem was a rupture of the cooling tower on the roof. Since then, air-conditioning has been provided by temporary air-cooled chillers, which cost $30,000 a month each to rent, Mr. Brattain said, and two more will be brought in for the summer months. A new system is supposed to be installed in the spring of 2017.