The first step will be taken this week when Sir Ian is told formally, in writing, that his contract will not be renewed when it expires in February 2010, sources said.
Whitehall sources revealed that the Scotland Yard commissioner will be told to resign if the inquest, due to start later this month, concludes that the death of the innocent Brazilian should have been avoided.
The Daily Mail reported that a contingency plan has already been drawn up by Home Office officials in which Sir Ian's deputy, Sir Paul Stephenson, would be appointed acting Met Commissioner.
Assistant Commissioner John Yates, who led the ill-fated cash for honours inquiry, would be appointed acting number two in the Met under the plan.
One senior source said: "The grey suits are gathering. Ian has already been asked to consider whether his staying in the job is damaging the Met. The infighting at the top of the Yard is sapping the morale of the men and women doing the job on the street."
Sir Ian's leadership has been dogged by controversy, and has become increasingly precarious in recent years, with three serious challenges to his authority over the summer.
Assistant Commissioner Tarique Ghaffur has accused him of racial discrimination and started employment tribunal proceedings. Sir Ian is also at the centre of an inquiry into allegations that he influenced the award of police contracts to a close friend.
The inquest into the death of de Menezes, who was shot seven times in the head after being mistaken for a suicide bomber at Stockwell, South London, in July 2005, is expected to be hugely damaging for the Met.
A number of senior officers outside London are regarded as qualified for the role. Sir Hugh Orde, Chief Constable of Northern Ireland, Sir Norman Bettison, police chief in West Yorkshire, and Bernard Hogan-Howe in Merseyside would all be expected to compete for the post.