Pro-China President Mohamed Muizzu won office last year while campaigning on a promise to downgrade ties with India, and has since reoriented the strategically placed archipelago nation towards Beijing.
After coming to power he demanded the withdrawal of at least 89 Indian soldiers who had been stationed in the territory to assist with maritime patrols.
This week, the Maldives government said more than half of the garrison had left the country ahead of the Friday deadline it had set.
Despite the dispute, foreign minister Moosa Zameer struck a conciliatory note during an official visit to New Delhi on Thursday, saying his trip marked a "new initiative of collaboration, symbolising enduring friendship and shared goals".
Indian foreign minister S. Jaishankar said both countries had a common interest in reaching "an understanding on how best we take our relationship forward."
The Indian troops were operating three reconnaissance aircraft New Delhi had gifted the Maldives to patrol its vast maritime boundary.
Indian foreign ministry spokesman Randhir Jaiswal said on Thursday that two batches of Indian troops had already left the Maldives and been replaced by civilian "technical personnel".
He did not say whether the troop withdrawal had been completed.
"Both Maldives and India, they have been engaged for quite some time to see how best they can continue the operation of the aviation platforms," he told reporters in New Delhi.
"The first and second batch of our people who were providing support there, they had come back," he added.
The Maldives is a small nation of 1,192 tiny coral islets scattered 800 kilometres (500 miles) across the equator, but it strategically straddles key east-west international shipping routes.
India is suspicious of China's growing presence in the Indian Ocean and its influence in the Maldives as well as in neighbouring Sri Lanka.
Muizzu's government has entered several agreements with Beijing to boost bilateral relations and economic ties, sidelining India, which considers the tiny nation to be within its sphere of influence.
The Maldives signed a military assistance pact with China in March as the Indian garrison began leaving.
Its defence ministry said the deal was to foster "stronger bilateral ties" and that China would train its staff under the pact.
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