Facebook had admitted that 335 people in India were directly affected through an app installation.
The government has sought an explanation from Facebook by June 20, on reports that it shared information of users with mobile device makers.
Taking suo motu note of reports, the IT Ministry has also asked for a detailed factual report.
"Ministry of Electronics & Information Technology has sought an explanation from Facebook seeking a detailed factual report on the issue," an official statement said.
Reports claim that Facebook has agreements, which allow phone and other device manufacturers to access its users' personal information, including that of their friends without their explicit consent.
"The Government of India is deeply concerned about reports of such lapses and violations," the statement said.
It said that in response to earlier notices about breaches of personal data relating to the Cambridge Analytica episode, Facebook had apologized and assured the government that it would sincerely protect the data of users.
"However, such reports raise uncomfortable questions about the assurances made by Facebook," the statement said.
In case of data leaks to Cambridge Analytica, Facebook had admitted that 335 people in India were directly affected through an app installation, and another 5,62,120 people were potentially affected as friends of those users.