His resgination also led to the former Sports Minister Kate Hoey stepping down as the President of the Clay Pigeon Shooting Association (CPSA).
Boakes had told London 2012 officials earlier this month that he accepted their argument that it was not possible to stage the sport at the National Shooting Centre in Bisley.
But he was forced to withdraw his statement after British Shooting's Board of Directors objected.
The organisation, the governing body for all target shooting within Britain, continue to want the venue moved from the Royal Artillery Barracks at Woolwich to Bisley to ensure that shooting is left with a legacy after the Games have been held.
Boakes had tried to retain the support of British Shooting's directors by issuing a statement earlier this week.
He said: "British Shooting continues to seek a shooting venue for London 2012 which is a permanent 'bricks and mortar' legacy.
"British Shooting therefore wish to make it crystal clear that their preferred option is to host the 2012 shooting event at Bisley."
But even that was not enough to save him and he has now stepped down.
Officials in Britain are also out of their step with the sport's world governing body.
Earlier this week, as reported exclusively on insidethegames, Horst Schreiber, the secretary general of the International Shooting Sport Federation (ISSF), backed Woolwich as a venue claiming it offered a unique opportunity for the sport to be showcased at the Olympics.
He also said that he did not want the venue moved to Bisley because "[we] do not want to be somewhere isolated outside London with only a satellite village."
Hoey has now resigned in support of Boakes, who is also the chief executive of the CPSA.
The Labour MP, who advises London Mayor Boris Johnson on the Olympics, has described the decision to force Boakes to step down as "short-sighted and wrong".
British Shooting has suffered a troubled build-up to London 2012 under Boakes.
Besides the bitter row over Woolwich, he has also had to campaign for Britain's draconian pistol laws, introduced after the Dunblane Massacre in 1996 and which he claimed is preventing many of the country's potential Olympians preparing for the 2012 Games, to be lifted.
The sport has also had to cope with 78 per cent funding cutbacks after it failed to win a medal at last year's Olympics in Beijing.
Out of the team of five, only Richard Faulds qualified for the final.
Their budget for London 2012 was slashed to just £1.225 million, leading to number of athletes the sport funds to be slashed from 46 to just five and John Leighton-Dyson, the performance director, being made redundant.
Boakes was tonight unavailable for comment.