Saudi Arabia says it is an "outrage" that a US report about the 11 September attacks has raised suspicions about Saudi involvement.
Saudi Arabia requested the unscheduled meeting with Mr Bush
Foreign Minister Prince Saud al-Faisal also expressed dismay at a US refusal to publish a classified section of a report into the attacks, and launched a strongly-worded defence of his country's record in fighting terrorism.
Leaks to the US media have left little doubt that the missing pages relate to allegations about Saudi support and involvement in the 11 September plot.
The Saudi foreign minister had a hastily arranged meeting with the US president on Tuesday in the hope of persuading Washington to declassify the pages and allow the Saudis to respond.
However, Mr Bush justified his decision not to declassify citing fears that revealing the information would "help the enemy" by compromising intelligence sources and methods while investigations continued.
Meanwhile, Washington have asked for Saudi permission to question a Saudi man - Omar al-Bayoumi - who allegedly has links to two of the 11 September hijackers based in San Diego.
And in a separate development, US authorities have warned airlines and law enforcement agencies that al-Qaeda may attempt new
suicide hijackings sometime during the next few months.
Since the Congressional report came out last week, Saudi Arabia has said repeatedly it has nothing to hide but cannot defend itself against rumours.
"Twenty-eight blank pages are now considered substantial evidence to proclaim the guilt of a country that has been a true friend and partner of the United States for over 60 years," said Prince al-Faisal.
Fifteen of the 19 hijackers who used planes to attack New York and Washington were Saudi nationals and there have been allegations that some were also funded from Riyadh.
But Prince Saud said Saudi Arabia was "wrongly and morbidly" accused of complicity in the attacks by those with
Thousands died in the 11 September attacks
He stopped short of criticising the Bush administration, saying only that his country was "disappointed" at the decision not to publish but understood the reasons.
However, senators who compiled the 11 September report have also argued there was no reason not to declassify almost all of the information in the section dealing with foreign governments.
The chairman of the Senate Select Committee on Intelligence, Democratic Senator Bob Graham, said releasing the report would "allow the American people to make their own judgement about who are our true friends and allies in the war on terrorism".
The US Department of Homeland Security warned on Tuesday of possible 11 September-style attacks in late summer, using planes as weapons.
US interests at home and abroad could be vulnerable, the department said, and it named the UK, Italy, Australia or the US east coast as possible targets.
The advice is said to be based on information gleaned from interviews of at least one al-Qaeda prisoner as well as intercepted communications.
"We advised airline and law enforcement personnel to take a look at all their practices and initiate additional
measures they may feel are necessary," said Gordon Johndroe, spokesman for the department.
However, the terror alert level in the US remains unchanged at "yellow" or "elevated".