The move comes hours after a court in southern Tamil Nadu state refused a request by China's Bytedance Technology to suspend a ban on its TikTok app, putting its future in one of its key markets in doubt.
Following which, the centre had sent a letter to Apple and Google to abide by the high court's order, according to an IT ministry official.
However, the very next day, Google removed the TikTok listing from the Play Store and commented on the matter as under: "As a policy, we don't comment on individual apps, but adhere to the law in countries we operate in".
Earlier, TikTok had released a statement saying that the company is committed to improve and add new moderation features in order to curb misuse of their platform. The case is up for hearing in the Madras High Court, after which the SC will decide on its fate on 22nd April.
TikTok is a video making app, which allows users to create and share short videos with special effects.
At the time of writing this article, TikTok was still available in the Google Play Store and Apple's App Store. The app was globally ranked third amongst the most installed apps during the first quarter of 2019.
TikTok is problematic because it has been found to host user-generated content that is considered to be inappropriate.
Jokes, clips and footage related to India's thriving movie industry dominate the TikTok platform, along with memes and videos in which youngsters, some scantily clad, lip-sync and dance to popular music.