New Delhi considers the strategically located Indian Ocean archipelago -- which straddles key global shipping lanes -- to be within its sphere of influence.
But the Maldives has shifted into the orbit of China -- its largest external creditor -- with September's election of new President Mohamed Muizzu, who demanded the Indian troops leave.
Male's foreign ministry said New Delhi had agreed at talks in the Indian capital to start pulling out its 89 personnel by March 10, and complete the process within two months.
The troops are deployed to operate three Indian-donated maritime reconnaissance aircraft, two helicopters and a fixed-wing plane which have also been used for medical evacuations from remote islets scattered for some 800 kilometres (500 miles) across the equator.
The two sides had "reviewed" their co-operation with a view to "enhancing" their partnership in defence, security and other fields, the Maldivian foreign ministry statement said.
But the Indian government's statement on the meeting made no explicit reference to any withdrawal.
The two had "agreed on a set of mutually workable solutions to enable continued operation of Indian aviation platforms that provide humanitarian and medevac services to the people of Maldives", New Delhi's foreign ministry said.
Official sources in the Maldives said it was likely that the aircraft will remain in the nation of 1,192 coral islands, but could be operated by civilian Indian staff.
Tensions between the neighbours flared last month after three of Muizzu's junior ministers reportedly called Indian Prime Minister Narendra Modi a "clown" and a "terrorist" in since-deleted social media posts.
In another development, the Maldives defence ministry accused India's coastguard of entering its exclusive economic zone and harassing fishermen in three Maldivian trawlers.
The defence ministry said it called for an "explanation" from New Delhi after coastguard personnel boarded the three boats on Wednesday.
The incident came as Indian celebrities urged compatriots to boycott the island nation and instead book their next holidays closer to home.
Tourism accounts for nearly a third of the Maldives's economy, with Indians making up the largest share of foreign arrivals.
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