Ministry spokesperson Raveesh Kumar also made it clear that India's relation with Sri Lanka "stand on its own and is not dependent on our relations with any third country."
He said India was confident of the strength of enduring ties with Sri Lanka which were deep-rooted and multidimensional.
"We continue to take up with Sri Lanka issues related to the security concerns in the region and expect that our Sri Lankan friends will keep in mind our security concerns and sensitivities," he said.
The port, overlooking the Indian Ocean, is expected to play a key role in China's Belt and Road initiative, which will link ports and roads between China and Europe.
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In order to allay India's security concerns over the Chinese Navy's presence in Sri Lanka, Wickremesinghe had earlier ruled out the possibility of the strategic port being used as a "military base" by any foreign country.
Kumar also said that India attaches the highest importance to its relations with Maldives.
Noting that India has seen reports about the Maldives- China agreement and the reports have also alluded to the manner in which the FTA was passed by the Majlis, he said it will not be appropriate for him to comment on the contents.
He also said India was committed to supporting democracy, development and stability in Maldives.
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