Federline, 41, will have 70 percent custody of sons Sean Preston, 13, and Jayden James, 12, to Spears' 30 percent going forward.
Sources told the site that the exes have had the arrangement since roughly last August, but that it was only formalized in court recently.
Spears' custody of Sean and Jayden will not require supervision.
Federline and Spears, 37, previously shared 50-50 custody of their boys.
Spears filed for divorce from the former dancer in November 2006. The split was settled in March 2007. At the time, Federline maintained custody of the children until Spears stabilized after her widely-publicized breakdown.
A rep for Spears did not immediately return Fox News' request for comment.
The "Baby One More Time" singer has reportedly been struggling with her mental health recently.
In April, Spears checked into a mental health facility, reportedly due to the stress of her father Jamie Spears' illness. Britney slammed reports that she was committed against her will before leaving treatment at the end of that month.
Jamie has been Britney's conservator since her 2008 breakdown. In May, a judge in Britney's conservatorship case ordered a 730 evaluation, a process usually used to determine the mental health and competence of a parent in a divorce case. It is not clear for whom the evaluation was planned.
In May, Britney's longtime manager, Larry Rudolph, claimed that Britney's medications stopped working around the time that Jamie fell ill and that the singer simply needed a break from working.
"I don't want her to work again 'till she's ready, physically, mentally and passionately," Rudolph said. "If that time never comes again it will never come again. I have no desire or ability to make her work again. I am only here for her when she wants to work. And, if she ever does want to work again, I'm here to tell her if it's a good idea or a bad idea."