Before that court ruling was issued last year, the comptroller’s office completed audits of 18 charter schools around the state. Fourteen had significant financial irregularities, including one school that spent $67,951 on staff trips to the Caribbean, according to officials.

“We don’t have enough oversight, and that is clear,” said State Senator Bill Perkins, a Harlem Democrat and charter critic. “I’m not suggesting that this is rampant, but it undermines the integrity of the public’s faith in charters.”

Several New York agencies can issue charters: the State Board of Regents, the State University of New York and, in New York City, the city’s Education Department. In other cities, local school boards also have the ability to allow charter schools to open.

The issue of accountability has emerged as a major sticking point in negotiations over the bill, which would raise the cap on charters to 460 from 200. The bill has been passed by the Senate but remains stalled in the Assembly.

Even as the Obama administration promotes charter schools as integral to its education agenda, the inspector general in the federal Education Department has raised concern about growing accusations of financial fraud at schools around the country.

In New York, the Merrick Academy in Queens, which was founded by State Senator Malcolm A. Smith, has been subpoenaed by federal prosecutors over the possible misuse of school money to benefit Mr. Smith. Mr. Smith, who is no longer affiliated with the school, has denied wrongdoing.

State officials acknowledge the need for better oversight, and the State Education Department has reorganized the office that reviews charter schools. The goal, said Sally Bachofer, who now heads the office that oversees charters, is to hold “schools to high academic and operational standards.”