The Prime Minister's comments came on the same day that the Football Association of Wales confirmed that pounds 3.2m of FA funds promised to it by Kelly and FA chairman Keith Wiseman - who has refused to resign over the affair - would have been "a gift" that would never have needed repaying.
"The money was a gift to the football community of Wales," John Hughes the president of FAW, said.
He denied allegations that a condition for receiving the money was that its payment would secure Welsh support for Wiseman's bid to become a vice- president of Fifa, world football's governing body.
He added, however: "We said in order that the FA have a strong case for their World Cup bid for 2006 it would be good for Mr Wiseman to be involved. What we've done is completely above board."
The Welsh football authorities were told last Friday that the pounds 3.2m would not be paid as the gift had not been sanctioned by the FA's finance committee. It will now receive pounds 900,000 over three years instead of the pounds 3.2m over six to eight years, according to Hughes.
A spokesman for Fifa said the affair should not unduly damage England's bid to host the 2006 event. "It is obviously primarily an internal matter for the English FA and it is up to them to put their house in order. Our partners around the world are associations, not individuals. Most institutions have turmoil from time to time," he said.
He added that bids for 2006, in any case, will be judged not only on the input of national associations, but also on governments, police forces, tele- communications companies, broadcasters and everyone who might be involved in staging the event.
The Prime Minister's support came in Parliament yesterday as he was due to question the Sports Minister, Tony Banks, on the expensive globetrotting in support of England's bid that he has undertaken as part of the pounds 9m, three-year campaign to bring the tournament to this country. He chose instead to steer a diplomatic course and support the bid.
Banks himself admitted that Germany, another country hoping to host the 2006 event, would be happy with the crisis in the FA. "If I was a German I would be delighted with all the speculation" he said.
Sir Bobby Charlton, in Bangkok to promote England's 2006 bid at the Asian Games, said: "I don't think it makes any difference to us, to be honest.
"We know what we're doing, we have a good bid. If there are problems internally with the Football Association, we have to step back and just let it unfold."
Sir Geoff Hurst, whose hat-trick won the World Cup last time England hosted it in 1966, said: "It is unfortunate but I don't think it will have any long-term effect. I am confident that once these events are over there will be no damage."
Alec McGiven, the England 2006 bid director, said: "We're determined to prove to the world that England will provide the best venue for the tournament. We have a very strong case and have no intention of being deflected from it."
The FA succession issue,
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