The Ministry of Communications said Wednesday the account under the username Alpatuni was pornographic, which violated the law on information and electronic transactions.
It was closed after the communications minister wrote a warning letter to Instagram, the ministry said.
The comics depicted gay characters facing discrimination and abuse, which has become increasingly common in Indonesia since late 2015 when conservative politicians and religious leaders began a campaign of portraying lesbian, gay, bisexual and transgender people as a threat to the nation.
An account of the same name on Facebook, which owns Instagram, was also no longer accessible.
The ministry said it appreciated that members of the community reported the account, which "accelerated" its removal.
Indonesian netizens in turn congratulated the ministry. On Twitter, Fahmi Alfansi Pane, a policy analyst at the Indonesian parliament, thanked officials for "acting decisively" to protect public morality but also told The Associated Press he had never seen the comics.
The government frequently threatens to block Western social media and Internet companies for content deemed illegal but has never taken such measures, possibly fearful of a public backlash due to the hugeAd popularity of the services with Indonesians.
In 2017, it briefly and partially blocked the Telegram messaging app because of its failure to remove groups linked to violent jihad.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)