The £10 million bid was placed nearly 12 months ago, after years of planning by engineers from British Waterways - owners of the unique structure.
But because the proposed visitor centre at the lift is a new building it isn't allowed any cash from the Heritage Fund - even though the boat lift itself is 123 years old.
A spokesman for British Waterways said: "We don't feel negative. To get a successful bid is pretty unusual and we've seen problems up and down the country where new building elements are involved.
"We had a very supportive letter from the fund and we are still in the frame. So our first priority is to work on this and get the bid re-submitted. We are not going to hang about."
The next application could be ready within the next two months.
It's hoped the proposed centre will offer an income for the boat lift's upkeep.
And alternative funding will now have to be found for the visitor centre - hopefully from European funding and sponsorship.
The 100ft high Victorian landmark, the first ever boat lift of its kind, has been closed for safety reasons since 1983.
The Anderton Boat Lift Trust was launched in October 1994 to bring together all sectors of society in the restoration project.
It is made up of British Waterways, the borough and county councils, The Mid Cheshire Chamber of Commerce, Trade and Industry and other interested groups.
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