BOA chief Andy Hunt insists it is in 'robust' shape
The British Olympic Association made a £1.5m loss last year and needed the organising committee for London 2012 to step in, the BBC has learned.
Revelations that Locog made a £2m payment to help keep the BOA afloat came ahead of Wednesday's BOA AGM.
The loss follows a deficit of £1.3m in the preceding year.
However the BOA said the money was merely an advance, adding that the BOA is in "robust" financial shape.
BOA chief executive Andy Hunt told BBC Sport: "Locog advanced us £2m that they would be paying us in July 2009 anyway so although it's termed a loan, it's money they would have paid us, so there's nothing strange about it.
"It was just a good business decision to ask Locog to do this. The BOA is in a robust financial position.
"2008 was a very unusual year - because it was a Games year, revenue was substantially greater, nearly £10m greater than the previous year, which is not unusual when you're taking Team GB out to a summer Olympics, particularly on the other side of the world.
An artist's impression of the Olympic Stadium in Stratford, east London
"And secondly, the executive board took a decision to go through a process of completely modernising the organisation.
"To do this, they had to undertake some restructuring charges of £1m, which was - in [chairman] Colin Moynihan's words - 'the best investment made by the organisation in the last 105 years' to allow us to get in good shape for 2012."
The BOA and Locog have a Joint Marketing Programme Agreement, which is worth about £30m to the BOA over the seven-year period leading up to 2012.
That £2m payment had not been due until 1 July 2009, but was given in advance, with 4% interest subtracted, in order to ease the BOA's cash flow problems.
Some senior figures in British sport have expressed shock that the BOA was having to pay interest to Locog - one describing it as "The Bank of Locog".
A spokeswoman for Locog refused to comment, insisting that this was a matter for the BOA.
As reported by BBC Sport's James Pearce on Tuesday, the BOA's annual financial report for 2008 revealed that £368,000 was spent on consultants alone.
Locog advanced us £2m that they would be paying us in July 2009 anyway so although it's termed a loan, it's money they would have paid us, so there's nothing strange about it
BOA chief executive Andy Hunt
Some leading figures in Olympic sport have also raised questions about the amount of money being spent by former England rugby union coach Sir Clive Woodward, who has been an employee of the BOA since his spell as performance director at Southampton Football Club.
Woodward's BOA coaching academy is still without a sponsor and those who raise concerns about his role argue that the BOA should be concentrating on its core activities instead.
Meanwhile, the BOA and the British Paralympic Association will be based under one roof at a new central London headquarters from September.
The two organisations will remain independent bodies but the BOA will leave their current home in Wandsworth while the BPA, also known as ParalympicsGB, will move from the offices they share with UK Sport.
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