Documents were seized from the homes and police stations of 14 serving and five retired officers in a series of dawn raids.
About 90 officers, led by the Metropolitan police's internal investigation squad, CIB3, acted after allegations of corruption that include taking bribes, drug dealing, destroying evidence, and taking pounds 350,000 from an armed robbery.
In addition to the twelve men already suspended, two more serving officers face suspension after the raids and five former Flying Squad officers were targeted in the operation. No one has yet been arrested, but police are studying the seized documents. Computer software is also believed to have been confiscated.
The operation at 6.30am yesterday follows a three-year investigation into the unit and comes shortly after two Flying Squad officers turned supergrasses. The corruption allegations go back seven years. The squad, which investigates armed robberies in Greater London, gained notoriety from the 1970s TV series The Sweeney.
The inquiry centres on the squad's offices in Walthamstow, north-east London. Half of those suspended work in Walthamstow, while the other half used to but have moved to other posts.
Yesterday's raids across London and the Home Counties targeted officers ranging in rank from detective constable to detective chief inspector. The anti-corruption branch is currently investigating a criminal's claims that officers helped themselves to pounds 350,000 from an armed raid.
A member of the Flying Squad and two former members of the unit were arrested last month and charged with breaking into the home of a drug dealer and with conspiracy to supply cannabis with a street value of pounds 500,000.
The serving officer and one of the former officers have turned informers and been moved from prison to a safe house. They claim up to 30 officers are corrupt.
It is part of on-going anti corruption drive instigated by Sir Paul Condon, the Metropolitan Police Commissioner, who said that there may be up to 250 dishonest officers in his force. A special 45-strong squad, called CIB3, was set up earlier this month to actively target suspect officers.
Deputy Commissioner Sir Brian Hayes said: "[The] operation is part of a proactive on-going inquiry into allegations of serious corruption dating back over some six or seven years. It reinforces the Commissioner's commitment to upholding honesty and integrity in the Metropolitan Police."
A Scotland Yard spokeswoman said there could be further suspensions but admitted it was limited in the action it could take against retired officers.