The ratification sends a strong signal that Prime Minister Narendra Modi, elected by a landslide last month, wants to bolster strategic and trade ties with the United States when he meets President Barack Obama in Washington in September.
"I can confirm that we are ratifying the Additional Protocol to the IAEA Safeguards Agreement," said Syed Akbaruddin, spokesman for the Ministry of External Affairs.
The move signals India's commitment "to the responsible use of nuclear power", Akbaruddin added, confirming earlier domestic reports. No comment was available from the IAEA.
Yet critics say the pact fails to address concerns that India could as a result get its foot in the door of a club of countries that trade in nuclear materials, without first signing a treaty that seeks to curb the spread of nuclear weapons.
There would be "no gain for non-proliferation" said Tariq Rauf, a former senior IAEA official now at the Stockholm International Peace Research Institute.
India, which first tested a nuclear weapon in 1974, is not a party to the Non-Proliferation Treaty. That means its military nuclear programme is not subject to inspections by the IAEA, the United Nations nuclear watchdog.
Both India and Pakistan tested nuclear weapons in 1998, setting off an arms race between neighbours that have fought three wars since independence. That in turn has raised tensions with Asian superpower China, Pakistan's patron.
In a report last week, a defence research group said one Indian enrichment facility was undergoing an expansion and could be capable of producing a large surplus of weapons-grade uranium from mid-2015.
The plant would be able to produce an estimated 160 kg of weapons grade uranium a year - enough for five atom bombs - in excess of the needs of India's planned fleet of nuclear-powered submarines, IHS Jane's said.
Indian officials have shown displeasure over the report, with a newspaper quoting one saying it was "mischievously" timed to influence a meeting this week of the 48-member Nuclear Suppliers Group (NSG) in the Argentinian capital Buenos Aires.
Following the U.S.-India nuclear deal, the IAEA in 2009 approved the Additional Protocol, intended to clear the way for the NSG to grant India a waiver to trade with other countries in the civilian nuclear field.
Ratification is a key step towards separating India's civilian and military nuclear operations, and could help unlock tens of billions of dollars in U.S.-led investment in new nuclear generation capacity.
Yet as recently as a year ago, talks on India joining the group were being slowed by the prospect that its accession might trigger similar demands by other countries that have not signed the NPT, such as Pakistan, to join.
"India sees its ratification of its Additional Protocol as an arrow in its quiver supporting its quest for NSG membership," said Mark Hibbs, a nuclear expert at U.S. think-tank the Carnegie Endowment.
But the lack of verification of India's weapons programme, which contrasts with tighter controls on NPT signatories, would continue to be a concern.
"India's entire nuclear weapons programme is totally outside the scope of its Additional Protocol," Hibbs added. "It isn't clear to most people what the utility of the Additional Protocol in India is as a verification instrument."