London Marathon Limited, the trading subsidiary of the London Marathon Charitable Trust Limited, gave £4.5m of the £17.8m raised in 2009 to the trust.
Tracing the Marathon's Millions, which will be broadcast at 8pm, will claim that the remainder is "eaten up in salaries and undisclosed costs".
It also says one member of staff, which London Marathon Limited refuses to identify, was paid between £240,000 and £250,000 last year.
Nick Bitel, chief executive of London Marathon Limited, said the documentary displayed "stunning ignorance" of charity trading and that the marathon generated more money for charity than any other running event in Europe.
The marathon's costs include toilets, barriers, venue hire, staff and rent. He said its costs compared favourably with other, similar events.
"This is an attack on charity trading companies," said Bitel.
He would not reveal the identity of the highest-earning employee, but said the person's salary last year included a one-off bonus for saving the marathon £3m by finding a new sponsor without using a sponsorship agency.
David Bedford, race director of the marathon, said the programme displayed "a toxic mixture of opinions and half-truths masquerading as facts".
This year's London Marathon is on 25 April.