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The deal allows the US to use seven bases to help with operations against drug trafficking and terrorism.
But it was criticised by other Latin American countries over a concern about the rise in US influence in the region.
The US, which has supplied Colombia with more than $7bn (£4.5bn) in aid since 2000, was forced to look for a new centre for regional operations after Ecuador refused to renew the lease on its military base at Manta.
The deal agreed by former President Alvaro Uribe in October 2009 gave the US access to the bases for 10 years and would see a maximum of 800 US military personnel and 600 civilian defence contractors based in Colombia.
They would operate the US aircraft that maintain 24-hour monitoring of the region, intercepting communications and coordinating with spy satellites to protect US interests.
But the court's chief justice Mauricio Gonzalez said the deal was "an arrangement which requires the State to take on new obligations as well as an extension of previous ones".
He said that as such, it should be "handled as an international treaty, that is, subject to congressional approval".
The court did not rule on the legitimacy of the agreement itself and the ruling does not mean the US has to leave the country altogether.
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| Juan Manuel Santos, Colombia's new president |
The ruling will, however, please many of Colombia's neighbours, says our correspondent, particularly President Hugo Chavez of Venezuela, who had repeatedly accused the US of planning to use the bases to invade his country and seize its oil reserves.
BBC News
