FBI chief Robert Mueller told the Associated Press that many of the plans had been stopped thanks to better intelligence-gathering and co-ordination, as well as information from al-Qaeda detainees.
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Without getting into details, we have thwarted a number of attacks, both large and small
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Robert Mueller, FBI chief
But Mr Mueller warned that many potential attackers remained at large in the US, and that it could take years "to win the war on al-Qaeda".
His comments follow a critical report by a Congressional panel, which concluded that the 11 September attacks could have been prevented if only all the clues had been put together and information shared among the numerous intelligence agencies.
Last month, the chairman of the Senate Intelligence Committee, Bob Graham, said the FBI was unprepared to prevent new terror strikes on US soil.
But speaking to AP on Saturday, Mr Mueller rejected calls for some of his bureau's duties to be transferred to a new agency.
Successes
He told AP that the FBI now had much better information-gathering technology and better channels of communication with the CIA and other US agencies.
"There have been any number of attacks on ships that have been thwarted," Mr Mueller said.
"Without getting into details, we have thwarted a number of attacks, both large and small."
FBI spokesman Bill Carter told the French news agency AFP that most of the attacks were not planned in the US, but some of them were intended to take place on American soil.
According to the official, the successes include:
Mr Mueller said he believed the US and its allies were "well on the way to winning the war".
But, he warned: "The fact of the matter is, it is a war. Al-Qaeda still has the capability of striking us."