Wembley's directors will be told on Tuesday that the national stadium's total losses totalled around £40million in its first year in operation.
Michael Jeffries, the chairman of Wembley National Stadium Ltd, the wholly-owned subsidiary of the FA, may also tell board members at a meeting on Tuesday he intends to stand down.
It is understood Jeffries has been troubled by illness recently and new FA chairman Lord Triesman is keen to take more control over the stadium's finances.
Jeffries' background in major construction projects made him an ideal chairman during the building of the stadium but FA chiefs now want someone more experienced in running a large-scale venue.
The financial losses come as a blow to the FA but they are not unexpected after large start-up costs and a huge bill for increased security.
In terms of revenue, Wembley made a loss of around £22million but with interest payments on the £346million outstanding loan the overall figure is around £40million.
The FA are confident, however, that Wembley will generate large profits for the organisation in the future.
Triesman last week outlined to the FA board his plans for refinancing the loan that was taken out to build the £800million stadium. Negotiations with the banks are now expected to start in earnest.
An FA source said: "Staffing costs will be lower in the future and we will claw all that money back."
The FA do have the record £425million TV contract with ITV and Setanta, which comes on stream next season, to fall back on.