The attacks came as a shock, the 9/11 commission said
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US President George W Bush says he has asked Congress to create a new post of national intelligence director.
Mr Bush also announced the creation of a national counter-terrorism centre to collect and analyse data on suspected terrorist activities.
The move comes in response to calls to overhaul US intelligence made last month by the commission investigating the 11 September 2001 attacks.
Mr Bush said his administration would go beyond the proposals.
"We are a nation in danger," Mr Bush said, and the work of securing the US was not yet done.
The latest warning of possible attacks on three US cities was a solemn reminder of the threats the country continued to face, he said.
But the Democrat Party challenger for the White House immediately criticised the president for failing to understand the urgency of quick action.
"The time to act is now, not later," John Kerry said, urging Mr Bush should to call Congress back from its summer recess to begin working on the changes.
"Here we are today almost three years after 11 September and we still don't have a national director of intelligence," Mr Kerry said while campaigning.
Congressional check
The Democratic contender endorsed all the proposals of the 9/11 Commission.
But Mr Bush was hesitant until it became clear that the political pressure to act was irresistible, says the BBC's Martin Turner in Washington.
And there is a key difference between what he announced and what the commission called for, our correspondent says.
The commission had urged the establishment of a cabinet-level post which would have the authority to force the often warring intelligence agencies to co-operate and share information.
Instead President Bush said the new director would oversee the work of the intelligence agencies but would be placed outside the White House.
President Bush also gave no indication of how to streamline the congressional committees that oversee the work of the intelligence community, our correspondent adds.
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I don't think that the office should be in the White House, however, I think it should be a stand-alone group to better coordinate
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"I will hire the person and I can fire the person. I don't think that the office should be in the White House, however, I think it should be a stand-alone group to better co-ordinate," Mr Bush said.
Mr Kerry criticised this move, saying: "You give greater power and leverage to the person who is the national director if they are seen as speaking directly for the president within the White House.
"You also co-ordinate more effectively with the other agencies that you need to co-ordinate in order to summon the greatest possible response to protect Americans."
The bipartisan commission's report last month blamed intelligence bodies for failing to predict or avert the airliner hijackings, in which nearly 3,000 people died.