Some 21 million girls in India are "unwanted" and receive fewer resources because their parents wanted a son, the government said, as analysts called for action to boost women's earnings.
The government's annual economic survey, presented to parliament on Monday with a pink cover, included a chapter on women's issues for the first time - emblazoned #MeToo in recognition of the global campaign against sexual harassment.
"India must confront the societal preference, even meta-preference for a son, which appears inoculated to development," it said.
While India is set to regain its position as the world's fastest growing major economy, development "has not proved to be an antidote" for its skewed sex ratio, lack of women in the workplace and low contraceptive use, the survey said.
A sex ratio of 943 females per 1,000 males has led to the identification of some 63 million "missing" women, it said.
While sex-selection abortions are widely prevalent despite a ban, the preference for sons also manifests in parents choosing to keep having children until they have sons, leading to an estimated 21 million "unwanted" girls, the survey noted.
"Consigning these odious categories to history soon should be society's objective," it said.
"A son 'meta' preference ... may be detrimental to female children because it may lead to fewer resources devoted to them."
Many parents prefer sons because they can inherit property while families have to pay dowries when their daughters marry.
Only 24% of women in India were employed in 2015-16 and almost 47% do not use any contraception, it said.
Analysts welcomed the government's acknowledgement of the challenges to gender justice, but said it must do more to ensure equal rights for women.
"There is no recognition of the failure of economic policy with respect to women's rights and women's work - including unpaid labour," said Jayati Ghosh, a professor of economics at the Jawaharlal Nehru University in Delhi.
"They are also not doing enough to stop violence against women, which is seriously limiting women's labour participation," she told the Thomson Reuters Foundation.
Nearly two-thirds of Indian women with college degrees are without jobs, and female labour force participation is among the lowest in the world, according to World Bank data.
Ensuring property rights for women, and ending gender stereotyping in Indian popular culture can also help, said women's rights activist Kamla Bhasin.
"It is not just the government; we need to tackle the entrenched patriarchy at every level. Otherwise, the message is: women are not equal to men."