During the interaction, the Prime Minister recalled his first such interaction with the Secretaries, in June 2014.
But Yameen's election loss last September has seen the new administration under President Ibrahim Mohamed Solih gravitate back to the nation's traditional benefactors in New Delhi.
The reported clarification by the persons to the newspaper, reflect the deep differences between the Sri Lankan PM and President and the widening rift within their coalition government.
India is considered a key partner in the United States' Indo-Pacific strategy, as outlined by a recent Pentagon report that notes how both countries share a "common outlook" in the region. India is committed to helping the Maldives in every way possible, he added.
China also considers the Maldives an important route in its Belt and Road Initiative (BRI) that, apart from its other projects, also aims to connect the Indian Ocean to Central Asia. Modi also stopped at the Kochchikade Church to leave flowers and pray for those who lost their lives in the tragic Easter Sunday attacks.
He called terrorism was the biggest threat facing the world and there could be no distinction between the so-called "good" and "bad" terrorists.
The leaders pledged to combat piracy, terrorism, organized crime and trafficking through "coordinated patrolling and aerial surveillance, exchange of information, and capacity building", the statement said.
During his visit, India and the Maldives agreed to set up a joint working group on counterterrorism, countering violent extremism and deradicalization.
He also said that Modi's visit to Sri Lanka, following the lifting of the travel advisories by many countries including the UK, France and China, will serve as a boost for the tourism industry.
Interacting with all Secretaries to the Union Government at his residence in New Delhi yesterday Mr Modi said all departments of the government must seek to leverage the upcoming milestone of 75 years of independence.
On arriving in Lanka from Maldives, the Prime Minister tweeted: "Happy to be back in Sri Lanka, my third visit to this attractive island in four years".
The Maldives mended ties with India with Solih's election as president a year ago.
Modi was in the Maldives on his first official overseas trip since being elected to a second term.
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