In December, Manson was caught with an LG flip phone under his mattress and had used it several times before officers discovered it, Terry Thornton, according to spokeswoman for the California Department of Corrections.
This latest discovery was made on Jan. 6 in a highly protected area inside the prison, the CDCR confirmed.
Manson has been issued a rules violation for possession of a contraband cell phone. He has a right to appeal, the decision.
Manson lost 30 days credit for his previous rules violation.
An investigation is under way to determine how the cell phone was smuggled into the prison and into Manson's cell.
The now 76-year-old orchestrated one of the most notorious killing sprees in U.S. history.
Actress Sharon Tate was among the seven victims in 1969.
Manson has been locked up for more than three decades and will likely die behind bars.
He is currently housed at Corcoran State Prison.
In 2009, nearly 7,000 cell phones were discovered in California prisons. The number this year is above 8,000.
Officials say prisoners use smuggled cell phones for a range of criminal activity, including running drug rings and planning escapes. In some cases, prison guards have been accused of bringing the phones into prisons and selling them for as much as $1,000 a piece.
This summer, President Obama signed a bill banning cell phones from federal prisons and making it a crime to smuggle one in. That law does not apply to state institutions.