The meeting was held behind closed doors on Friday and was part of an ongoing two-day visit by Putin to India's capital New Delhi, Press TV reported.
The two leaders also oversaw the signing of a number of other agreements that covered areas such as economic and regional issues. Another key agreement involved cooperating over India's plan for a manned space mission.
India has witnessed an expanding space program, with the Indian Space Research Organization carrying out 97 spacecraft missions and 68 launch missions since its establishment in 1969.
The agreement that would allow Russia to build nuclear plants in India was unprecedented as it contradicted Delhi's previous policy of following the India-US Civil Nuclear Agreement framework that was signed in 2005.
The agreement which was signed during the tenure of former US president George W. Bush effectively led to Washington's decision to recognize India as a nuclear weapons power. Based on it, the two countries had agreed to develop six US-designed reactors in India in 2016.
India's purchase of Russia S-400 air defense system came amid earlier warnings from Washington over buying Russian arms which it had already said would be in violation of the sanctions against buying weapons from Moscow.
India has, however, signaled that it will ask Washington for a special waiver from the sanctions, though a US official last week suggested there was no guarantee such waivers would be issued.
The US has already imposed sanctions on China for its Russian arms purchases and has further threatened Turkey that it would do the same if it finalizes its own S-400 deal.
Kremlin spokesman, Dmitry Peskov, has condemned the US government's ban against Russia's weapons sales, describing it as a dishonest competition "to squeeze the main competitor of US makers out of the markets”.