The state's swine flu vaccine program has been hampered because more than a third of the doses have been in the form of nasal spray, which can't be given to high-risk groups such as pregnant women and children with underlying medical problems.
That has been "really seriously limiting," said Claire Pospisil, a state health department spokeswoman.
The state's predicament is reflected nationally: Until now, the percentage of nasal spray shipped for use has been double that which the government had planned.
The situation in New York only began to improve last week, when the state received a shipment in which 85 percent of the doses were vials for shots, which high risk groups can take.
Last June, the federal government ordered 40 million doses of the nasal spray FluMist from MedImmune of Gaithersburg, Md. - or about 16 percent of the total the government has contracted for. The rest of the vaccine was supposed to be standard shots.
But MedImmune has been able to deliver more vaccine more quickly than the companies producing the vaccine for shots: They have had a harder time getting the vaccine to grow in chicken eggs. The result was that all of the state's first shipment of H1N1 vaccine was FluMist.
For the next four weeks, the shipments were 33 percent nasal spray. Finally, last week, came the shipment with just 15 percent nasal spray, Pospisil said.
Another problem: Most practitioners have registered with the state for the shot vaccine - not the nasal spray. A few health care providers who were sent nasal spray even called the state to say they couldn't use it, said Dr. Guthrie Birkhead, the state's deputy commissioner for public health.
The nasal spray uses a live, weakened form of the flu virus, and is approved for use only in those aged 2-49 who are healthy and not pregnant. Many of those most at risk for complications from swine flu cannot use it.
"If we had planned it, we wouldn't have planned it this way," Birkhead said. He added that "it would have been nice to know sooner" that manufacturers were having a hard time growing the vaccine for shots.
Birkhead said practitioners in the state have ordered about 7 million doses of vaccine and the state has so far gotten about 1.3 million doses.
The flood of nasal spray and lack of injectable vaccine has caused logistical problems for health care providers.
"We prefer regular vaccine for sure," said Terry Lynam, spokesman for North Shore-Long Island Jewish Health System. "For high-risk groups, you need the shot." Lynam said that 5,000 of the 21,000 doses of vaccine the health system has gotten have been nasal spray.
Birkhead said those who have gotten vaccine they couldn't use have been encouraged to pass it on to others who can, he said.
Tom Skinner, a spokesman for the federal Centers for Disease Control and Prevention, said the problem is not too much nasal spray, but too little vaccine. "I think we're looking at the big picture," he said. "We want more vaccine out there, period."
Dr. Robert Belshe, director of the Center for Vaccine Development at St. Louis University, said the nasal spray vaccine is especially good for healthy kids - who are also at high risk for swine flu. Studies have found it creates greater immunity than the shot in those 18 and under and it is quick and painless, said Belshe, who has been a consultant to MedImmune.