But the messages, which were in Arabic, were not translated until 12 September, US intelligence sources told the Washington Post.
"The match is about to begin" and "Tomorrow is zero hour" is what they are reported to have said.
Officials say that even if the communications had been translated on 10 September, they would not have provided enough information to prevent the attacks on New York and Washington in which about 3,000 people were killed.
The White House has complained about the disclosure of the messages, saying it can "potentially interfere or harm America's capacity to fight the war against terror".
NSA in the spotlight
The two messages were intercepted by the National Security Agency (NSA), responsible for intercepting and analysing communications.
National Security Agency
One of 13 US federal intelligence agencies
Based in Fort Meade, Maryland
Director: Lieutenant General Michael Hayden
Protects information sent through US Government equipment
Intercepts and deciphers foreign signals
Budget and staff numbers are secret
On Tuesday they were put before a congressional intelligence committee which is looking into events leading up to the attack and how intelligence agencies can avert future attacks.
Members of the panel are questioning senior FBI, CIA and NSA officials behind closed doors.
Lieutenant General Michael Hayden, the NSA director, was reportedly asked by the committee why it took his agency two days to translate the messages.
According to one legislator quoted by CNN, his response was that the agency collects a lot of information daily and it would be nearly impossible to translate all of it in a timely manner.
NSA analysts are still not certain who the messages were from, according to sources quoted in the Washington Post.
Some reports in the American media suggest the communications were sent from Afghanistan to Saudi Arabia.
The CIA and FBI have been heavily criticised for not sharing intelligence leading up to the 11 September attacks.
The two Arabic messages have now put the NSA under the spotlight for the first time.