Wembley National Stadium Limited is expected to report a loss of more than £20m for its first year of operation.
Football Association sources insist the £800m stadium will eventually generate large profits but concede losses are again expected next year.
Including interest payments on the £346m loan, Tuesday's WNSL board meeting is set to be presented with a pre-tax deficit of around £40million.
The loss stems from heavy start-up costs in the first year of operating.
"Building Wembley was always a considerable financial risk for the FA," said BBC Radio 5 Live sports news correspondent Gordon Farquhar.
"They are banking on it producing a steady revenue stream in order to pay for their activities like investing in the game's grassroots and running the representative teams.
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"The first year loss is, according to sources at the FA, down to start-up costs and bringing in extra security."
WNSL's accounts are due to be published in mid-May, before which the board is set to receive an update on refinancing negotiations for the outstanding loan, which was taken out in 2002 to pay for the stadium's construction.
The refinancing deal, over which the FA is reported to be holding talks with WestLB and Barclays to reduce interest on the loan from 8% to 7%, indicates the banks believe the company is a viable proposition.
With new broadcast rights deals worth over £550m, and there being no limit on the number of events Wembley hosts, the FA's finances appear to be in good health.
"Before approving the project, FA board members knew that if they got the sums wrong, then the cost of running the stadium would divert money away from the FA's core activities of investing in the game's grass roots and running the England teams," added Farquhar.
"Get it right, however, and the stadium could become a cash cow for the future.
"The FA believes the losses will be relatively short-term: it has the comfort of a vastly improved TV rights deal which has brought millions more into the coffers.
"And FA chairman Lord Triesman has outlined plans for a refinancing of the stadium debt, which should help reduce outgoings in the coming years."
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