He lost the verified blue badge after he changed his username from @rajeev_mp to @Rajeev_GoI. The blue badge was restored within a few hours.
Chandrasekhar had taken charge as the MoS of the IT ministry last week.
According to Twitter's verification policy, if an account holder changes the username, Twitter may automatically remove the blue verified badge from an account.
The microblogging platform said it was in touch with the minister's office and had worked swiftly to restore the verified blue badge.
The development also comes at a time when Twitter is locked in a tussle with the government over the new social media rules. The brief loss of the blue badge triggered criticism from some netizens.
Last month, Twitter found itself on a sticky ground after the personal accounts of Vice President M Venkaiah Naidu and RSS chief Mohan Bhagwat lost their verified blue tick marks briefly. Twitter, at that time, had said the blue badge and verified status could be automatically removed from an account if it is incomplete or inactive for six months as per its rules.
The coveted 'blue badge' helps users distinguish the authenticity of accounts that are of high public interest, and gives Twitter users more context about who they're having conversations with, the microblogging platform had said earlier.
Twitter has been at loggerheads with the Indian government over its failure to comply with the IT rules, despite repeated reminders. Twitter -- which has an estimated 1.75 crore users in India -- lost its legal shield as an intermediary in the country, becoming liable for users posting any unlawful content.
Amid tensions with the government, Twitter has appointed a resident grievance officer days after it designated a chief compliance officer, and also released its first India Transparency Report on Sunday to comply with the new IT rules.
The US social media giant's website has listed Vinay Prakash as the new grievance officer, providing contact details and procedures for users to report potential violations of its rules and terms.
Meanwhile, former IT Minister Ravi Shankar Prasad tweeted that it is "assuring to note that Twitter too has taken some steps to comply with the new rules".
He also lauded the new IT Minister Ashwini Vaishnaw for firmly reiterating that the new IT rules are designed to empower the safety and security of users against misuse and redress their grievances.
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