Until now, the city’s rate of closing for charters — about 4 percent since the first charters were granted in 1999 — was below the national average: 15 percent of charters across the country have been closed since 1992, according to a report by the Center for Education Reform, published last December.

By the city’s standards, Peninsula was not the worst charter school, nor was it the best. Last year, 46 percent of Peninsula’s students passed the state English exam, a better performance than 47 other city charters. On the math exam, 60 percent of its students scored as proficient. For the last four years, it received C’s on its annual progress reports. It was, by definition, in the middle of the herd. But not on Far Rockaway, where those scores were high enough for Peninsula Prep to outperform 9 of the 10 elementary schools its students are zoned for.

Ericka Wala, Peninsula’s principal since July 2009, said the school had been improving, though slowly.

“We were a struggling school in 2009 when everybody was A’s and B’s,” Ms. Wala said, “and when they raised the standard, we were able to maintain a C. The scores had to have gone up in order to do that. I do feel the school is being used as a warning.”

New York City has closed charter schools for poor performance in the past, but their test scores were dismal. In other cases, schools were closed after they had already been damaged by poor fiscal or management decisions. Last year, the city succeeded in closing the Ross Global Academy, a charter school led by Courtney Sale Ross, the multimillionaire widow of Steve Ross, the Time Warner chief executive. When the city announced plans to close the school, only 26 percent of its students had passed the state English test and 33 percent passed math.

James Merriman, chief executive of the New York City Charter School Center, said a confluence of factors might have led the city to raise the bar for renewing charter schools. In 2010, state education officials toughened the math and English exams administered annually to students in third through eighth grades, after years of complaints about test score inflation. Across the city, scores dropped precipitously, and suddenly schools that once appeared to be holding their own were actually found to be in distress.

Another factor is that as more charter schools reach their five-year renewal points, the city is judging them by their progress report grades, which were not given to schools opened and renewed before the reports began in 2008. The additional measurement affected Peninsula Prep, which failed to meet five of nine standards it had promised to reach, according to the city’s renewal report. One of the standards was receiving at least a B on its progress report.