The fire was extinguished within 45 minutes at the Bhabha Atomic Research Center on the outskirts of Mumbai, India's financial and entertainment capital, the center's spokesman, S.K. Malhotra, said in a statement.
"It may be noted that no nuclear reactor, radioactivity or radiation is involved in the accident," Malhotra said.
Police were investigating the cause of the fire, he said.
Firefighters found two bodies charred beyond recognition in a third-floor room of the modular laboratory, he said.
The Bhabha center has a number of nuclear reactors and the research involves both nuclear weapons and nuclear power. It was set up in 1954 and named after a top Indian scientist, Homi J. Bhabha.
The fire occurred on a day Japan's new prime minister offered to consider selling nuclear power technology to India despite differences over signing a test ban treaty.
Energy-starved India is interested in wooing Japan's thriving nuclear power industry, but Tokyo has so far not allowed Japanese companies to do business in nuclear reactors and fuels until New Delhi agrees to stop conducting nuclear tests.
In New Delhi, Japanese Prime Minister Yukio Hatoyama told reporters that his government would examine the matter following assurances by Prime Minister Manmohan Singh that India would not divert any imports from Japan for weapons purposes or to third countries.
"The two prime ministers shared the view that nuclear energy can play an important role as a safe, sustainable and nonpolluting source of energy in meeting the rising global energy demands," said a joint statement.
India has so far rejected calls for it to sign the Comprehensive Test Ban Treaty, but a U.S. nuclear accord with India last year reversed more than three decades of U.S. policy barring the sale of nuclear fuel and technology to India since its first atomic test in 1974.
Singh stressed that India has unilaterally declared a moratorium on nuclear testing. Its last test was in 1998.
India currently has 17 civilian nuclear reactors. It gets just 3 percent of its energy from nuclear power. It plans to increase its nuclear capacity to 63,000 megawatts by 2030 from 4,120 megawatts today.