The amount raised for the cause fell from 629,181 in 2008-9 to 233,099 in 2009-10, newly-published accounts filed to Companies House show.
More than 421,000 was spent on the campaign to locate Madeleine and merchandise costs last year, leaving the balance standing at 470,034 at the end of March.
The McCanns spoke last month of their fears that the dwindling of the fund would leave them unable to continue paying private detectives to search for their daughter.
Since then they have signed a lucrative deal to write a book about Madeleine's disappearance, with all proceeds going to the fund.
Madeleine's Fund was launched a fortnight after the little girl vanished from her family's holiday apartment in Praia da Luz, southern Portugal, on 3 May, 2007.
Donations flooded in from supporters around the world who wanted to do something to help her parents, and the income for 2007-8 totalled 1,846,178.
The fund's directors wrote in a preface to the 2009-10 accounts: "Income in the new financial year is lower than last year and we continue to review all our expenses to ensure value for money. As anticipated, the costs of the search during the year continue to be higher than the annual income."