Security firm G4S has not been paid since July 13, Locog chief executive Paul Deighton has told MPs.
The firm has so far been paid £89 to £90 million by organisers but the rest is "up for negotiation", he told the Commons Home Affairs Select Committee.
G4S told organisers on July 11 that it would not be able to provide enough security staff for the Olympics - just over two weeks before the Games started.
Troops and police were drafted in at the last minute to plug the gaps - at their worst the shortage of staff provided by G4S was 35%.
Mr Deighton said the whole contract with the company was worth £236 million, including a £57 million "project management fee".
This included 15% profit for the company, and the rest was mainly the wages of a team who were in charge of recruiting and training staff. He was asked by committee chairman Keith Vaz: "You have paid £89 to £90 million, all public money, and the rest is up for negotiation, which you will have with them?"
Mr Deighton replied: "Yes."
At best the shortages of G4S staff were 4% and at worst 35% during the Olympics, he told the committee.
Nearly two-thirds of venues saw a shortfall of more than 15%, although they were up to capacity during the transition period and the Paralympics.
London 2012 chairman Sebastian Coe told the committee: "It is difficult to look beyond their inability to deliver on the contracted number of security personnel that we were consistently assured by them that they would be able to deliver."