The Jan. 6 discovery is the second time in two years Manson was found with a cellphone, Corcoran State Prison officials said.
In March 2009, Manson called people in California, New Jersey and Florida with an LG Electronics flip phone guards found under his prison bunk, spokeswoman Terry Thornton told the Los Angeles Times.
The Times said at the time it was not known if Manson had used the phone for criminal purposes.
Thornton wouldn't say how Manson got the phone this time or whom he called, if anyone, saying the case was under investigation.
Manson, 76, was charged with violating prison rules, but not with a crime, because California has no law prohibiting inmates from possessing phones.
Thirty days were added to his sentence for the first offense, officials said.
Manson, originally sentenced to death, is serving a life sentence and is eligible to reapply for parole in 2012.
He was found guilty of conspiracy to commit the ritualistic murders of "Valley of the Dolls" actress Sharon Tate, wife of film director Roman Polanski, and six others in 1969.