A Reuters review of regulatory filings and interviews with people familiar with different firms' practices show the calculation varies widely even among the top private equity firms.
Blackstone Group, Carlyle Group, and Bain Capital, for example, do not include money that comes from general partners in average net IRR calculations, while Apollo Global Management does, the review shows.
Read MoreApparel retailers don't make good private equity targets
Fund marketing documents are not public, but the sources said all these firms disclose to investors whether they include general partner capital in the calculation or not.
The SEC's review comes after the agency put together a dedicated group earlier this year to examine private equity and hedge funds that had to register with it as part of the 2010 Dodd-Frank financial reform law, Reuters first reported in April.
Much of the SEC's focus so far had been on fees that private equity funds charge. In a May 6 speech, Andrew J. Bowden, director of the SEC's Office of Compliance Inspections and Examinations, said more than half of the private equity funds the agency examined had inappropriately allocated expenses and collected fees.
The average net IRR figure is crucial to investors' understanding of their actual profits from private equity funds. That's because not all investors in a fund pay the same amount of fees to the private equity firm for managing their money.