The bench hearing the case said: "It is evident from media reports that pornography and inappropriate contents are made available in this kind of cyber applications".
And the moves in India to ban Tiktok are the latest in a string of woes for the popular app. Earlier this year, the US Federal Trade Commission fined the company $5.7 million over child privacy violations.
A spokesman for TikTok in India declined to comment on the app's removal resulting from the TikTok ban in India, saying the matter was still in the courts.
TikTok users in India who had previously downloaded the app on their phones were still able to use the service on Wednesday.
The order passed by the High Court is based on various unsubstantiated and factually incorrect or gross exaggerations made by the PIL litigant, the petitioner company states.
The issue will be heard in the Supreme Court on April 22, but the app could potentially vanish from stores before then.
While Apple and Google are yet to comment on the directive, TikTok said in a statement: "We are committed to continuously enhancing our existing measures and introducing additional technical and moderation processes as a part of our ongoing commitment to our users in India". The next hearing on April 24th.
In its court filing, ByteDance argued that a "very minuscule" proportion of TikTok content was considered inappropriate or obscene.
Reacting to the top court's refusal to stay the high court's order, TikTok said: "We have faith in the Indian Judicial system and the stipulations afforded to social media platforms by the Information Technology (Intermediaries Guidelines) Rules, 2011.We have been stepping up efforts to take down objectionable content".
"The said ban, if not lifted immediately, shall cause severe prejudice and irreparable harm to the Petitioner Company and result in competitors gaining a significant and potentially irreversible advantage over the petitioner company".