By STEPHANIE STROM

State and federal officials are starting to take their knives to the pay of leaders of nonprofit groups they do business with to help share the pain of tighter budgets.

A provision in New Jersey’s recently passed budget, for example, includes a limit on what nonprofit groups can pay their chief executives if they are providing social services under state contracts. The cap, based on a formula that also applies to for-profits providing such services on behalf of the state, is part of a broader effort by Gov. Chris Christie to rein in salaries on state workers.

In New Hampshire, Attorney General Michael A. Delaney is investigating compensation among nonprofit hospital executives. And Vermont legislators are trying various ways of curbing salaries paid by nonprofit groups that have contracts with the state.

On Capitol Hill, four senators this spring refused to approve a $425 million package of federal grants for the Boys & Girls Clubs of America after staff members looked at the organization’s tax forms as part of a routine vetting process and were surprised to learn that the organization paid its chief executive almost $1 million in 2008 — $510,774 in salary and bonus and $477,817 in retirement and other benefits.

“A nearly $1 million salary and benefit package for a nonprofit executive is not only questionable on its face but also raises questions about how the organization manages its finances in other areas,” said Senator Tom Coburn, Republican of Oklahoma.

Another senator, Charles E. Grassley, Republican of Iowa, has told Treasury Secretary Timothy F. Geithner that he is concerned that the Internal Revenue Service is not tough enough in policing pay in the nonprofit sector and that regulations governing compensation are too weak.

“I’ve asked him to review these regulations to see how they can be made effective,” Mr. Grassley said. “What’s there now doesn’t seem to be working.”

Mr. Grassley, who has used his seat on the Finance Committee to scrutinize a wide variety of nonprofit practices, noted that pay had been a “major issue” in his reviews over the last several years of universities, charitable hospitals and the Smithsonian Institution.

Compensation has long been a point of controversy among donors to nonprofits. By far the biggest category of complaints posted on the Web site of Charity Navigator, which offers research and analysis of nonprofit groups, involves complaints about pay.

“Many donors feel that paying the leader of a charity a six-figure salary is outrageous,” said Ken Berger, the group’s president.

Mr. Berger disagrees with the argument, popular among many nonprofits, that to attract top talent to manage complex organizations, they must compete with for-profit businesses.

“I’m not advocating poverty wages,” he said. “But arguing that those working for the benefit of the neediest people in our society should make millions and multimillions like corporate leaders defies common sense.”

Most charities pay their leaders far less than corporate executives. Large charities like the Boys & Girls Clubs and the American Cancer Society, which take in more than $100 million annually and tend to pay their leaders six-figure incomes, account for just two-tenths of 1 percent of the nation’s more than one million nonprofit groups, according to Charity Navigator.

And many nonprofit groups, including cultural institutions, have cut compensation for their leaders as endowment values, donations and other income have plunged.

The compensation awarded to nonprofit leaders follows no discernible pattern, even among similar types of nonprofits.

Roxanne Spillett, the chief executive of Boys & Girls Clubs, was paid $988,591 in 2008, a year in which the organization took in $107 million. Dr. Jennifer Howse, chief executive of the March of Dimes, was paid a total of $627,104 by her organization, which raised $237 million.

Compensation also varies by type of nonprofit. Museum directors and hospital chiefs generally are better paid than leaders of other nonprofits. Median compensation among the organizations that participated in the Chronicle of Philanthropy’s annual survey examining pay at the wealthiest charities and foundations was $361,538 in 2008 — but the median compensation among hospital executives was $848,802.

There are no clear rules for the I.R.S. to assess pay at nonprofits. Organizations it questions can make their case using opinions from compensation consultants, among other things.

“These are done on a case-by-case basis and are heavily reliant on comparisons,” said Marcus S. Owens, a lawyer and former head of the division of the I.R.S. that oversees nonprofits.

Many organizations are reluctant to discuss pay. A dozen organizations contacted in recent weeks about their compensation policies said officials were not available to comment.

Rick Goings, who sits on the Boys & Girls Clubs board and was on the committee that established its compensation policies, said he found the senators’ attack on Ms. Spillett’s compensation “offensive.”

Mr. Goings noted that during Ms. Spillett’s 14-year tenure as chief executive, the number of clubs had risen to 4,000 from 800 and the combined revenue of the national office and the local clubs jumped to $1.4 billion from $438 million.

“They don’t seem to appreciate that the Boys & Girls Clubs today are a fairly sophisticated business run by fairly sophisticated business people,” said Mr. Goings, who is also chief executive of Tupperware Brands. “Do they really think we’d waste their money? Or anyone’s money?”

The senators’ scrutiny over Ms. Spillett’s salary has mushroomed into a wide-ranging inquiry in which they are now questioning Boys & Girls Clubs investments in private equity and offshore funds and its use of its endowment.

In an interview, Ms. Spillett, joined by Mr. Goings, choked up when she was asked what had happened the day the senators first raised the issue of her compensation. “I can’t talk about it,” she whispered, tears in her eyes.

She said the day had been the worst she could remember. “I have worked in the organization for 32 years, and I’ve never been motivated by a dime, not for a single minute,” she said.

She said she had contacted board members and demanded that they stop putting money into her supplemental retirement plan, which gave the impression that she took home more than she actually did. “I said, “Forget it, take it away,’ ” Ms. Spillett said. “I cannot watch our movement get hurt by this. I don’t want it to hurt our ability to help kids.”

Mr. Goings said the board had reluctantly agreed. “We felt that would be sending a signal to these guys that we did something wrong — and we didn’t,” he said, referring to the senators. “We really pushed back, but Roxanne pushed harder.”

He said the pressure from the senators would make it harder to recruit a successor for Ms. Spillett, who is close to retiring.

The American Heart Association determines compensation in much the same way as the Boys & Girls Clubs, using comparative data, consultants’ opinions and reviews measuring performance against various benchmarks. In 2008, the heart association paid its longtime chief executive, M. Cass Wheeler, who was retiring, a total of $995,424. That year, the association raised $645 million.

Bill Achenbach, the heart association’s executive vice president for human resources, said Mr. Wheeler’s compensation figure was distorted by payments to a supplemental retirement plan. Supplemental retirement plans also are part of Ms. Spillett’s and other nonprofit executives’ compensation.

Mr. Achenbach said Mr. Wheeler’s work for the organization justified his compensation. In his 15 years at the helm, Mr. Wheeler pulled all of its affiliates under the national organization’s legal umbrella, sharply increased its fund-raising and took on a new role as a highly visible advocate, Mr. Achenbach said.

“I would say he changed the face of the American Heart Association,” he said. “He really moved the organization to a much better place.”

For his part, Mr. Wheeler said compensation was the wrong measure of an organization.

“The question people should be asking is, Is the organization effective, is it accomplishing real results?” he said. “Once they get an answer to that question, they can put compensation into some kind of context and then decide whether it is appropriate.”

As for his own compensation, Mr. Wheeler said it looked higher than it was due to extraordinary payments related to his retirement.

“If you peeled all that back, you’d get to a base salary less than $600,000,” he said.