There was something wrong in each of the four issues of The Bennett that students at the Frank Sinatra School of the Arts High School produced last year. Or at least that is what the assistant principal thought. Before they went to press, she edited 50 percent to 75 percent of the articles in each issue of the student newspaper. Everything from punctuation to a review of a school performance was fair game for the administrator’s red pen.

“My students got to the point that they were saying, ‘Why should we do this? They are going to cut it anyway,’ ” said The Bennett’s adviser, Taisha Matthews.

Like many other public school newspapers in New York City, The Bennett is subject to prior review, meaning the administration has the right to read the newspaper before it is printed. Some principals use that opportunity to paint the school in a more flattering light.

Many student journalists and newspaper advisers see this as censorship. Principals and other school leaders say it is part of their responsibility to make sure students are not harming the school or one another with their words.

The assistant principal at Frank Sinatra insists that she does not censor the newspaper; she sees herself, she said, as helping Ms. Matthews catch the errors she missed.

First Amendment disputes like this are playing out every day in classrooms in New York City, where only about half of the 509 public high schools even have student newspapers, compared with 74 percent nationwide, according to a 2009 study by Jessica Siegel at Brooklyn College.

The number has gone up slightly since 2007, but high staff turnover and the opening, closing and other reorganization of the schools makes the progress hard to measure.

There are several reasons many New York City schools do not have student newspapers: budgets are tight, the strong emphasis is on high-stakes standardized tests and many of the city’s high schools are new and have limited resources.

“They have to worry about filling the classrooms and hiring teachers before they can focus on a school newspaper,” Ms. Siegel said.

But teachers and experts say that when schools have student newspapers, students and advisers often get mixed messages from the school administration about what they can and cannot publish.

Some of that is natural: young people want more freedom. A nationwide study by the Knight Foundation found that nearly twice as many students as their teachers believed their newspaper should be published freely.

“What we often hear is that principals want to see the paper before it gets published but they don’t know what they are looking for,” said Rob Schimenz, president of the New York City Scholastic Press Association. “They assume they can change whatever they want."

Many principals are reviewing articles, and in some cases prohibiting them from being published, according to Mr. Schimenz and others.

When Nancy Kaplan advised The International Insider at the College of Staten Island High School for International Studies, her principal pulled an opinion article about the Middle East crisis. One student wrote from an Israeli perspective, a second student from the Palestinian view. The principal found the article unbalanced and told Ms. Kaplan to cut it.

For the most part, student publications are filled with articles about award winners and movie reviews, but newspaper staffs still feel pressure from the administration to paint the school in a positive light.

“Even though we aren’t supposed to be censoring our words, we are,” said Deborah Kosnar, 16, a news editor at The Blazer, at the World Journalism Preparatory Academy.

And that self-censorship is a troubling consequence, according to the Student Press Law Center.

“Ultimately it is the most worrisome outcome,” said the center’s executive director, Frank LoMonte, “when students internalize it and just start censoring themselves.”

The inexperience — and vulnerability — of advisers also play a role. It is not uncommon for schools to “dump the newspaper on the new hire,” said Starr Sackstein, the New York State regional director of the Journalism Education Association and adviser to The Blazer.

“Untenured teachers fall prey, and it’s a cold thing for the administration to do.”

As a result, the teachers “end up unknowingly censoring themselves because they are trying to be responsible and safe and administrators exploit that, maybe not uncoincidentally,” Ms. Sackstein said.

This happened to Ms. Kaplan when she let her principal pull the Middle East opinion article.

“I was new and didn’t want to cause trouble,” said Ms. Kaplan, who is now a master teacher in East New York. "So I gave in."

Legally, high school newspapers are on a different footing than those outside the classroom. Unlike law governing commercial newspapers, the law for student journalists is murky when it comes to freedom of the press. In some cases prior review is allowed, in others it is unconstitutional. Either way, it is clear that principals have the final world on the level of First Amendment rights they grant their students.

“It is far and away the most common justification for censorship and it is the most illegitimate one,” Mr. LoMonte of the Student Press Law Center said. “It is legally and educationally unsound.”

Still, there are some schools in New York City that have made the separation between the main office and the newsroom an official part of school policy.

Editors at The Classic, the 23-year-old student paper at Townsend Harris High School, retain complete editorial control of their newspaper. Since 2001 the paper has had a signed agreement with the school’s administration assuring the students’ First Amendment rights.

Having an official charter is rare, but there are other schools, like Queens Vocational and Technical High School, where Mr. Schimenz teaches and where principals and advisers have a verbal agreement: as long as the newspaper is using ethical journalism practices, it is free to publish as it sees fit.

“The Classic is a lot stronger because we are self-sufficient,” said Sarah Mahmood, 19, a former editor in chief of the paper who is now a sophomore at Wellesley College. “We had a sense of responsibility.”

No matter which direction the school administration leans, students are affected by the process.

“It’s not giving us a chance to experience what real journalists experience,” said Ms. Kosnar, The Blazer editor. Her school does not have prior review, but she still feels that she is under the principal’s watchful eye. “To get that freedom of speech must feel real good, and we can’t have that feeling.”

Cases of principals exerting influence over high school newspapers have surfaced in private schools, but incidents at public high schools are rarely publicized because advisers fear the repercussions.

That, Mr. LoMonte said, makes student papers all the more relevant.

“If there is something wrong inside of the school, it is the school newspaper’s job to point that out,” he said, “’cause no other paper is going to.”