A report by the administrator of FA Cup finalists Portsmouth, now relegated and 119 million pounds in debt, included Begovic on a list of transfer fees owed with the explanation 'sell on fee Tottenham' next to his name.
Tottenham said in a statement on Thursday that the money was due to them, but disputed the explanation given by the administrator.
"The statement contained within the Administrator's report released yesterday... that it relates to a sell-on fee for Begovic, is inaccurate, as is the statement that the player was registered with Tottenham Hotspur," the club said on their website.
Tottenham said they had agreed to the joint purchase in the January transfer window of French centre-back Younes Kaboul, who had previously been at Spurs, and Bosnian international Begovic.
"The transfer of Younes Kaboul was completed and Portsmouth pressed for an immediate payment in order to alleviate their cashflow situation," added Tottenham.
"We were assured that the transfer of Begovic would be completed before the end of the transfer window.
"In order to assist Portsmouth with their financial difficulties we paid Portsmouth an agreed sum of money, whilst at the same time concluding an agreement that, should Begovic be sold or loaned to any Club other than ourselves, we would be repaid the sum of one million pounds."
Begovic, Portsmouth's number two keeper, subsequently moved to Stoke in a 3.25 million pound deal.
"Our intention had been to assist a fellow Club in financial difficulties whilst at the same time protecting our commercial position," said Tottenham in the statement. "We shall continue to do the latter."
Portsmouth administrator Andrew Andronikou, whose report detailed creditors including the milkman, a local florist and a pie company, said he had no further information from what had been published.
"You can draw your own conclusions... if it's due we'll pay it. As a football club, they will be paid I have no doubt," he told Reuters.
