The Los Angeles County Department of Child and Family Services determined Mueller's home was unsafe because she was using drugs again, the Los Angeles Times reported Friday.
"It just wasn't a stable environment with different nannies coming in and out, and child protective services came in and did their thing, and this is the outcome," a source close to Mueller told the New York Daily News. "Brooke didn't have a say in this."
The boys -- Bob and Max -- were placed in temporary custody with Richards, with whom Sheen has two daughters, 9-year-old Sam and 7-year-old Lola, the newspaper said.
"Charlie supports the actions of the Department of Children and Family Services," his rep told TMZ. "He knows Max and Bob are safe and in a stable, loving environment with Denise and the boys' sisters."
This is not the first time Richards has taken care of her ex-husband's children.
She watched over them late last year while Mueller was in rehab for substance abuse for the 19th time, the Times said.
"Brooke knows any time, and Charlie, that any time they need help with the boys, that I'm there," Richards told Radar Online at the Time.
Radar reported Mueller is refusing to go to rehab again.
"Brooke was given many opportunities... by social workers to clean up her act," a source, whose name was not reported, told Radar.