In a letter to housing minister John Healey, Johnson said the Government had "short-changed" London by redirecting to other regions funds previously earmarked to upgrade over 100,000 poor quality social housing units across London.
Johnson added that he would instruct the London region of the Homes and Communities Agency, which he chairs, to channel funding back into London's affordable housing programme over 2009/10-2010/11 to fill the hole in the budget so that the affordable homes could be revamped.
He said he the cash would come from additional resources announced by the Government for the HCA as part of the Prime Minister's £1.5 billion housing package, thereby re-routing the cash taken from London's budget back into the budget that was raided.
Johnson said: "As mayor it is my job to defend the capital's budgets and the city's poorest. I am looking at how I can use my powers to win back London's rightful share of new housing funds, and reverse those decisions that condemn many of London's poorest families to live in unacceptably poor conditions."
Johnson said the Government had not consulted the Greater London Authority or the London Boroughs over the plans to raid the capital's affordable housing budget and that the Greater London Authority was considering a legal challenge to the raid.
A Department for Communities and Local Government spokesman dismissed the possibility of a legal challenge and said the Government's £1.5 billion housing announcement meant that London was £200 million better off. "There is more money for London housing," he said. "John Healey is now looking for the Mayor to play his full part in ensuring that the new affordable housing that Londoners need is built this year and next."