Anjani Kumar, a Counsellor in India's UN Mission, announced the multi-year contribution at the 2017 UN Pledging Conference for Development Activities on Monday.
This contribution would be in addition to $10.582 million India is contributing to various other UN programmes, he said.
A total of $398.98 million was pledged by about 20 countries during Monday's conference session.
The Fund launched on June 8 is managed by the UN Office of South-South Cooperation (UNOSSC) and focuses on the least developed countries (LDCs) and Small Island Developing States (SIDS).
The $100 million that India is contributing is not earmarked "in the spirit of sustained predictable funding for SDGs and South-South Cooperation," Kumar said.
This means that unlike much of international aid that is tied to donors' interests, the utilisation of India's contributions will be flexible and attuned to the needs of the receiving countries.
Criticising the practice of donors earmarking their contributions, Kumar said it leads to the collective priorities of the UN being disregarded.
While the resources required for meeting the core UN mandates are stagnant and unable to keep up with multiplying demands on the system, the situation is made worse by the increasing mismatch between the earmarked and non-earmarked funding, he added.
He said, "India believes that the UN should have the necessary resources to finance its activities, in an appropriate and balanced manner."
"The first project from the Fund is being executed in partnership with seven Pacific Island countries," Kumar said. "The Fund has since then identified 15 more projects."
Of the $5 million India contributed to the Fund this year, $2 million would be utilised for reconstruction in Dominica and Antigua and Barbuda, which took a big hit from hurricanes, Kumar said.
The Fund project currently underway is an early warning system for extreme weather conditions for the Cook Islands, Kiribati, the Marshall Islands, Micronesia, Nauru, the Solomon Islands and Tonga.
When the Fund was launched in June, UNOSSC Director Jorge Chediek said that it was yet another example of India's contributions to "shaping a better world" and its "notable leadership and drive towards ensuring that no one is left behind, both in India and worldwide."
The $100 million contribution pledged to the Fund and $10.582 million to other programmes are in addition to the annual dues of about $35 million mandated by the General Assembly as India's contributions towards the UN's regular budget, the peacekeeping operations and the tribunals.
The contributions totaling $10.582 million are for the UN Development Programme ($4.5 million), World Food Programme ($1.92 million), UN Relief and Works Agency for Palestinians ($1.25 million), UN Women ($1 million), Unicef ($862, 000), UN Population Fund ($500,000), UN HABITAT ($150,000), UN Environment Programme ($100,000), UN Office on Drugs and Crime ($100,000) and Voluntary Fund for Technical Cooperation ($200,000).
Kumar said that India will also be making contributions to the trust funds for victims of torture and modern slavery, and to the programme for UN Volunteers.