Speaking on a visit to Sri Lanka, the atoll nation's new President Abdulla Yameen said he did not want to proceed with the Status of Forces Agreement (SOFA) that would have given the US a foothold in his archipelago located across the main east-west sea route.
"There have been discussions before... We are not going to pursue it," he told reporters in Colombo during his second overseas visit since winning elections two months ago.
Although the president gave no reason for the decision, Mohamed Shareef, a minister in Yameen's office, said it had been made over fears that the pact would upset its neighbours, including India.
"We have told them that we can't do it because both India and Sri Lanka are also not happy with it," said Shareef, without giving further details.
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Shareef said the proposed SOFA would have given the US military access to two atolls in the nation of 1,192 tiny coral islands scattered some 800 kilometres (500 miles) across the equator.
India is the regional super power and is highly sensitive to outside presence in the Indian Ocean area. It has also been recently involved in a diplomatic bust-up with the US over the treatment of one of its diplomats in New York.
Yameen's first foreign visit after his election was to New Delhi.
On his visit to Colombo, the president also said he was keen to resolve an ongoing commercial dispute with an Indian infrastructure company, GMR, which was kicked out of managing the Male airport in December 2012.
Yameen said he was also keen to expand the current airport to cater to increasing tourist traffic to the country which is an upmarket destination for well-healed holiday makers and honeymooners.
The country of 330,000 Sunni Muslims attracted some 1.2 million tourists last year, officials said.