Samaraweera was a key ally of Rajapakse during the 2005 presidential election campaign but fell out of favour after he criticised the president for giving his unelected brothers a big voice in policy-making.
The government announced in a statement the decision to strip the three men of security but did not comment on the move.
In a surprise step, the president on Friday dismissed former foreign minister Mangala Samaraweera (then aviation minister), national heritage minister Anura Bandaranaike and junior ports minister Sripathi Sooriyarachchi.
"He (Samaraweera) is now left with two police constables for security, despite writing to the police chief last week saying his life is under threat," Samaraweera's co-ordinating secretary, Ruwan Ferdinands, said.
A minister usually has around 30 security personnel, with the number increasing depending on the level of threat.
The sackings came a day after Bandaranaike, the brother of former president Chandrika Kumaratunga, declared that unnamed g