Spurs have confirmed the debt over the non-transfer of Begovic but have denied the figure relates to a sell-on fee.
The scale of Portsmouth's financial mismanagement was laid bare in detail on Wednesday as the club's administrators revealed debts totalling £119million.
The south coast club owe Spurs £1million after the proposed joint transfer of Younes Kaboul and Begovic to White Hart Lane fell through and the latter instead chose to join Stoke.
With Begovic never having been a Tottenham player, Spurs say the £1million amounts to compensation for the failure of the transfer rather than a sell-on fee.
The statement on the club's website read: "The club can confirm that it has invoiced Portsmouth Football Club for £1million in respect of the failure of the joint transfer of Younes Kaboul and Asmir Begovic to Spurs and in accordance with the Agreement of 30 January 2010 between both clubs.
"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 Football Club.
"Our original agreement with Portsmouth was for the purchase of two players for a combined, agreed price.
"The transfer of Younes Kaboul was completed and Portsmouth pressed for an immediate payment in order to alleviate their cashflow situation.
"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 £1million.
"Portsmouth were keen to openly and freely agree to this surety.
"Our intention had been to assist a fellow club in financial difficulties whilst at the same time protecting our commercial position.
"We shall continue to do the latter and trust that this statement clarifies the position."
Source: Team Talk
Source: Team Talk