A nonprofit foundation run by Harvard professor Henry Louis Gates Jr. is filing an amended 2007 tax return after it was found to have mischaracterized $11,000 in payments to officials as research grants.

Henry Louis Gates Jr.

Gates founded the Inkwell Foundation four years ago to conduct research and education about African and African-American history and culture. The foundation apparently reported a $10,000 grant to Joanne Kendall, the foundation’s treasurer, who is also Gates’ assistant at Harvard. In addition, the foundation made a $1,000 payment to secretary Abby Wolf that was mistakenly listed as research.

Gates told public interest journalism site ProPublica that the research grants were mischaracterized on the foundation’s Form 990. “It should have been listed as compensation,” he said.

Gates also told the Boston Globe that it was simply an error. “It’s a very minor issue, just a simple mistake from the account,’’ he said. “It will all be rectified, and all is well.’’

The foundation’s accountant admitted to ProPublica that he didn’t understand why the payments were misclassified, but that he planned to file an amended return in a week or so.

Gates was arrested on July 16 by Cambridge, Mass., police for disorderly conduct after an eyewitness reported a possible break-in at his home. The professor had been returning home after a trip abroad, and he and his driver found the front door to be jammed, so he needed to use the back door instead. The arrest provoked accusations of racial profiling, and the controversy ramped up after President Obama criticized the police for acting “stupidly” at a news conference last week. Charges against Gates were quickly dismissed, and Obama has invited Gates and the arresting officer, Sgt. James Crowley, to the White House for a beer to defuse the controversy.