The newspaper on Sunday, citing official documents, reported that agents of the Federal Bureau of Investigation gave personal airport escorts to two prominent Saudi families who fled the United States, while several other Saudis were allowed to leave the country without first being interviewed.
The Saudi families, in Los Angeles and Orlando, had requested the FBI escorts out of concern for their personal safety in the wake of the attacks.
The documents were obtained through a Freedom of Information Act lawsuit against the Justice Department by Judicial Watch, a conservative legal group, which provided copies to the Times.
FBI officials contacted by the daily reacted angrily to the allegation of preferential treatment for the Saudis.
One official, speaking on condition of anonymity, when queried by the Times about the airport escorts said "we'd do that for anybody if they felt they were threatened - we wouldn't characterise that as special treatment".
"We'd do that for anybody if they felt they were threatened - we wouldn't characterise that as special treatment"
Unnamed FBI official
The Saudis' chartered flights - arranged in the days after the 11 September 2001 attacks when most aircraft were still grounded – have long been a topic of allegations related to close family ties and associates of US President George Bush and the Saudi royal family.
The charges received their most prominent airing last year by the filmmaker Michael Moore, in his Fahrenheit 9/11 documentary.
White House officials have strongly denied any special treatment for the Saudis.