Sex-selective abortions have been outlawed but the practice has persisted, and national population data has consistently recorded one of the world's highest ratios of men to women.
But the latest National Family and Health Survey, released by the health ministry on Wednesday, recorded 1,020 women per 1,000 men after two years of research.
This is the first time any significant government population survey has shown more women than men in India, dating back to the first national census in 1876.
"The improvement in total sex ratio is positive and a step in the right direction but much still needs to be done towards gender equality," Population Foundation of India (PFI) health scientist Sanghamitra Singh told AFP.
The difference is explained by womens' longer life expectancy, with more boys still being born than girls -- 1,000 males for every 929 females.
"That could indicate some degree of son preference," Singh said.