Jamie has served as the 37-year-old pop star's conservator since her highly-publicized breakdown in 2007, and a source told E! News that she's scared his role in her life will hinder her access to her children.
"Britney is extremely anxious and paranoid about losing custody and she feels Jamie put her in jeopardy," the insider said, adding that the "Toxic" singer was furious with her father for allegedly putting hands on Sean Preston.
"Britney was very upset with her dad and left with the boys," the insider said. "She never wants Jamie to treat her boys the way he did or to get involved with disciplining them in that way."
The source added that Britney was the one to inform Federline, 41, of the incident, after which he went to police and was granted a restraining order on behalf of himself and their sons against Jamie.
A police report obtained by Us Weekly detailed an Aug. 24 incident involving Jamie, 61, and Sean Preston.
Sean and his younger brother, Jayden James, 12, were visiting their grandfather at his condo in California when he allegedly got into an argument with Jamie. He reportedly “felt unsafe” and locked himself in a room but Jamie managed to break in and allegedly “shook” the boy, a law enforcement source alleged.
Earlier this week, it was reported that Kevin had been granted 70 percent custody in a new agreement.
The exes previously shared 50-50 custody.
Despite Britney's fears, Kevin's attorney, Mark Vincent Kaplan, said Sean Preston and Jayden James will still see their mom.
“Kevin wants Britney to have meaningful and significant contact with their children,” Vincent Kaplan told Us Weekly. “Kevin has always maintained that position, and I commend him for that because he only wants what is best for the boys. He recognizes that includes having their mother as an active participant in their lives.”
Britney filed for divorce from the former dancer in November 2006. The split was settled in March 2007. At the time, Kevin maintained custody of the children until Britney stabilized after her widely-publicized breakdown.
In April, Britney checked into a mental health facility, reportedly due to the stress of her father Jamie's 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.
A rep for Britney did not immediately return a request for comment.
Fox News' Paulina Dedaj contributed to this report.