Former secretary of state Hillary Rodham Clinton speaks last year at a Clinton Foundation event. (Carolyn Kaster/AP)

Amid heightened scrutiny of the Clinton Foundation, two leading charity watchdogs have split in their assessments of the group’s spending practices.

One group earned headlines by placing the foundation on a "watch list" for potential donors, but in a new rating published Monday, the American Institute of Philanthropy's Charity Watch gave the foundation an "A" rating for financial performance. The group assessed that the foundation spent 89 percent of its 2013 expenses on charitable programs. The organization spent just 3 percent on costs associated with fundraising, Charity Watch found.

Last year, the same group gave the foundation an A+. President Daniel Borochoff said the slip resulted because the foundation spent 90 percent of its expenses on programs in 2012. He said that about 5 percent of the 600 charities his group rates get an A+; about 20 percent get an A.

[Clinton Foundation acknowledges missteps]

The "watch list" designation came from a second group, Charity Navigator, which cited potential issues that could concern donors. According to its Web site, Charity Navigator puts charities on the list whenever a third party identifies issues that potential donors might find interesting. It said it does not assess the merits of those accounts. In the case of the Clinton Foundation, it cited recent media accounts about foreign government donations.

Charity Navigator, which calls itself the nation's largest charity evaluator, has declined to issue a rating to the Clinton Foundation, citing the organization's "atypical business model." A spokeswoman for the organization did not respond to a request to elaborate on Monday. But Borochoff said the rival group uses an automated program to analyze the tax filings of charitable groups. The program does not allow analysis of the Clinton Foundation because the organization files a series of a tax returns for its different initiatives, he said.

A spokesman for the Clinton Foundation said its officials have been in "regular communication" with Charity Navigator in hopes that the group will refine its methodology and give the group a rating. He noted that Charity Navigator praised the foundation's donor disclosure in a letter last year.

On Sunday, the acting chief executive of the Clinton Foundation acknowledged that the $2 billion global philanthropy has made "mistakes," notably failing to disclose to the IRS that it received millions in foreign government donations over some years that coincided with Clinton's service as secretary of state. CEO Maura Pally said the organization's overall revenue figures have been accurately reported to the IRS.

The Charity Navigator designation was featured prominently in a New York Post story Monday, which also dissected the foundation's tax filing for 2013 and suggested that its spending is tilted toward administrative costs. For instance, according to the filing, the foundation spent $30 million in salaries and benefits and $8.7 million on rent and office expenses.

Borochoff said his organization looks at both tax filings and a charity's audited financial statement to analyze how much of spending goes to its charitable mission. He said, for instance, that an overall salary figure might be misleading — some salaries fund administrative workers, but other salaries go to charitable workers in the field. The Clinton Foundation has said that it employs 2,000 people around the world.

"Regardless of whether you like [Hillary Clinton's] politics or not, this is a good charity," he said.