Fifa general secretary Jerome Valcke has denied Jack Warner's claim in an e-mail that Mohamed Bin Hammam "bought" the 2022 World Cup finals for Qatar.
Suspended Fifa vice-president Warner made public the e-mail, which also questioned why Asian football boss Bin Hammam was running for Fifa president.
Valcke wrote: "[Hammam] thought you can buy Fifa as they bought the World Cup."
But in Valcke's denial he insisted he was not referring to any "purchase of votes or similar unethical behaviour".
"I'd like to clarify that I may use in an e-mail - a 'lighter' way of expression by nature - a much less formal tone than in any form of correspondence," said Valcke's statement.
"When I refer to the 2022 World Cup in that e-mail, what I wanted to say is that the winning bid used their financial strength to lobby for support.
"They were a candidate with a very important budget and have used it to heavily promote their bid all around the world in a very efficient manner.
"I have at no time made, or was intending to make, any reference to any purchase of votes or similar unethical behaviour."
The Qatar 2022 World Cup bid team has also issued a statement "categorically denying any wrongdoing" over the bid.
"We are urgently seeking clarification from Fifa about the statement from their general secretary," continued the Qatar officials' statement.
"In the meantime we are taking legal advice to consider our options."
Bin Hammam responded to Warner - and the publication of a dossier of evidence by American Fifa executive committee member Chuck Blazer, which sparked the suspension of both Bin Hammam and Warner - by publishing his own submissions to Fifa's ethics committee, whose decision it was to suspend him.
Bin Hammam argues he had no knowledge of any cash payments, and claims Blazer's dossier was published with the aim of influencing Wednesday's Fifa presidential election in incumbent Sepp Blatter's favour.
"Only a few days before the presidential election, [Blazer] submitted his written report," read a statement from Bin Hammam.
"That timing reveals the real purpose of the allegations, namely to influence the upcoming presidential election by discrediting Mr Bin Hammam and Mr Warner, the first being a candidate and the second being an influential person who has not yet taken a position as to which candidate he would support.
"This is a blunt abuse of the institution of the Fifa ethics committee."
As the then president of the Asian Football Confederation, Bin Hammam was technically neutral in the 2022 World Cup bid process as three other AFC nations, South Korea, Japan and Australia, were also in the running.
However, as a Qatari national, the 62-year-old openly supported his homeland with their successful bid.
Bin Hammam responded to Valcke's allegations that he "bought" the 2022 World Cup for Qatar by telling BBC Sport on Monday: "I don't know why he [Valcke] has said that."
Bin Hammam added: "If I was paying money for Qatar you also have to ask the 13 people who voted for Qatar."
When asked whether Valcke's allegation was true, Bin Hammam replied: "What do you think?"
Earlier Valcke stressed that his e-mail to Warner was intended to remain "private" and pointed out that Warner had only published selected parts of it.
"He [Warner] sent me an email asking if I want that [Bin Hammam to run for Fifa president], he said that I should ask Bin Hammam to pull out," Valcke added.
Valcke also denied that he had influenced Fifa's ethics committee, which suspended Warner and Bin Hammam on Sunday over separate allegations of bribery, pending further investigation.
The Fifa secretary general stated: "The first time I met the chairman of the ethics committee was yesterday [Sunday] at 1700 [BST] before we went to the press conference. I had no contact at all with anyone."
Bin Hammam was suspended a matter of hours after withdrawing from the Fifa presidential race on Sunday morning.
His decision leaves 75-year-old incumbent Blatter, who is seeking a fourth term in charge of the organisation he has run unopposed since 1998, as the only man running for the office.
Fifa has said its election will go ahead, as scheduled, on Wednesday.
Warner, who is president of the North, Central American and Caribbean confederation (Concacaf), has reacted angrily to the allegations of bribery and the Fifa ethics committee's decision to suspend him.
The Trinidad and Tobago government minister raged: "I look on the suspension as the worst form of justice by any sporting organisation.
"They came premeditated, they weren't prepared to listen, they were hand-picked to do a task and they did just that.
"The guys were hand-picked by Blatter. A kangaroo court would be a decent thing to say."
Warner, who also turned on Valcke, stated: "I wrote to Valcke telling him, among other things, that the outcome of the [Fifa presidential] elections may cause some fracture in the Arab world which we can ill afford now and that I will like to ask Bin Hammam to withdraw from the race.
"To which Jerome replied to me and I quote: 'For MBH [Mohamad Bin Hammam], I never understood why he was running. If really he thought he had a chance or just being an extreme way to express how much he does not like anymore JSB [Joseph Sepp Blatter].
"Or he thought you can buy Fifa as they [Qatar] bought the WC [World Cup]'."
Warner showed the e-mail to television crews and added: "You don't have to believe me, you don't have to like me, nobody has to eat with me, drink with me or sleep with me but Jesus Christ, take the truth when you see it."
Warner has also accused Blatter of making a gift of computers and an unauthorised $1m (£607,000) to Concacaf officials.
"I indicated that at the Miami Concacaf Congress on 3 May Mr Blatter made a gift of $1m to Concacaf to spend as it deems fit," Warner said in a statement.
"This annoyed [Uefa] president Michel Platini who was present and he approached secretary general Jerome Valcke complaining that Mr Blatter had no permission from the finance committee to make this gift to which Jerome replied that he will find the money for Mr Blatter.
"I also indicated Fifa, through Mr Blatter, organised gifts of laptops and projectors to all members of the Caribbean and no objections have been made today of this to date."
However, Platini said on Monday that he was having a joke with Blatter.
The Frenchman said: "He [Blatter] can give [to] the projects that he wants to give. I joke, I said 'but Sepp this was not accepted by the committee' - but he can give many projects to many national associations and we will confirm in the GOAL project after.
"In many Congresses for many, many years the president can give one or two projects to national associations - he has his own budget and he can give to one confederation and then it has to be approved of course by the executive committee next time."
Blatter has denied any wrongdoing as have Warner and Hammam, who are accused of offering financial incentives to members of the Caribbean Football Union.
In a file of evidence it was claimed bundles of cash of up to $40,000 (£24,200) were handed over to members of the CFU at the meeting in Trinidad on 10 and 11 May.
The payments were allegedly made to secure votes for Bin Hammam in his campaign to challenge Blatter for the presidency.
Bin Hammam effectively claimed Blatter was aware of some of the wrongdoing but the Fifa president did not report it, in itself a breach of Fifa's ethics code, but he was found to have no case to answer.
Meanwhile, independent Australian senator Nick Xenophon has demanded that Fifa refunds the Aus$45.6m (£29.6m) his country spent on their unsuccessful bid to host the 2022 World Cup.
Xenophon said: "It appears corrupt and highly questionable behaviour goes to the core of Fifa.
"Australia spent almost $46m on a bid we were never in the running for.
"Now we hear that bribes may have been made to fix the result for who will head up Fifa."
As vice president, China's Zhang Jilong will take charge of the AFC in the absence of Bin Hammam.
However, the decision to suspend Bin Hammam has been met with widespread criticism throughout the Middle East.
AFC vice president Yousuf al-Serkal, from neighbouring United Arab Emirates, said: "I think Bin Hammam has been mistreated.
"Bin Hammam is the right person who should have been elected to the presidency of Fifa from the point of view of change."