The president told Foreign Minister Sushma Swaraj that all nations should respect the Maldives' sovereignty, during her official visit to the capital Male to strengthen ties between the Indian Ocean neighbours.
"President Yameen stated that this government will not tolerate foreign parties to interfere with the country's domestic issues," his office said in a statement.
Yameen also "underscored that a country's integrity and national sovereignty must be respected by all", the statement said.
Yameen made no reference to the controversial conviction this year of former president Mohamed Nasheed, the country's main opposition leader, and his jailing for 13 years on terrorism charges.
Washington and others have strongly criticised his trial and a UN panel ruled last month that Nasheed's jailing was illegal and that he should be freed immediately.
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Swaraj released her own statement on Sunday at the end of the two-day visit, without mentioning Nasheed or the president's comments.
India spoke of strengthening ties and increasing defence cooperation with the Maldives, which is located across strategic international shipping lanes in the Indian Ocean.
The visit comes after Prime Minister Narendra Modi skipped the Maldives during his trip to Indian Ocean nations earlier this year as Nasheed was thrown in jail.
Last week Indian foreign affairs spokesman Vikas Swarup told reporters that New Delhi expected a "fair and just" resolution to Nasheed's jailing.
Supporters of Nasheed, the archipelago's first democratically-elected leader before being toppled in 2012, have maintained the conviction was part of a strategy by Yameen's regime to silence him.
The resulting political fallout has damaged the island's image as an idyllic honeymoon resort and brought crowds of protesters onto Male's streets.
Nasheed's high-profile legal team, which includes Amal Clooney, visited the former president in jail last month, further highlighting the case internationally.
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