The BBC quoted Transport for London (TfL), who would have funded the opening stages if the British capital had been chosen by Tour organisers Amaury Sport Organisation (ASO) as saying that it was pulling out.
London hosted a massively successful Grand Depart in 2007 and thousands again watched the end of last year's third stage near Buckingham Palace, following two hugely-successful stages in the north of England.
Boris Johnson, London's mayor, said on Tuesday that the estimated 35 million pounds outlay to host the start of the world's biggest cycling race could not be justified.
"I will not waste cycling money on something that would only deliver very brief benefits," he said on BBC London radio.
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"You've got to take some tough decisions in government and I think 35m quid on a one-off event was just not worth it for London."
Despite the snub, Prudhomme was not concerned.
"Contrary to what has been reported, we are not angry at all," he told Reuters.
"We are still grateful for the Grand Depart in 2007 and London pulling out does not change the fact that cycling is now big in Britain."
Prudhomme also added that the name of the city hosting the Grand Depart in 2017 would be unveiled "during the winter, just like we do every year".
"We were not just about to announce it as I read here and there," he explained.
The route for the 2016 Tour will be unveiled in Paris on Oct. 20.
(Reporting by Julien Pretot; Editing by Martyn Herman)
