The force insisted it has a "succession plan" to hand over the case to another experienced investigator when Detective Chief Inspector Clive Driscoll leaves in June.
Stephen's mother Doreen said she is "furious" that the first police officer she has trusted is being forced to leave his job.
DCI Driscoll is one of a number of officers with more than 30 years' experience who are being made to retire from the police due to their length of service.
Baroness Lawrence said: "I'm absolutely furious Clive is being taken off the investigation. It seems the clearest sign yet that the Met is planning on winding down the investigation and that is wrong.
"He is the first officer I have trusted and the only one to have delivered in the investigation."
She has asked to meet Met Commissioner Sir Bernard Hogan-Howe over the issue.
A Scotland Yard spokeswoman said: "DCI Driscoll is retiring from the Metropolitan Police Service (MPS) in June 2014 following over 30 years' service. The MPS remain firmly committed to retaining a dedicated team of detectives to continue the investigation into the death of Stephen Lawrence."
Stephen, an aspiring architect, was stabbed to death by a group of up to six killers in an unprovoked racist attack in Eltham, south-east London, with a friend on April 22 1993.
In January 2012 Gary Dobson and David Norris were jailed for his murder.