The app, which is owned by Chinese firm ByteDance, is facing growing scrutiny from Western authorities over concerns that China's government could use it to harvest people's data. Beijing has regularly denied having any such intentions.
The EU executive and the EU Council, which brings together representatives of the member states to set policy priorities, said on Thursday staff will also be required to remove TikTok from personal mobile devices that have access to corporate services.
TikTok, which has in the past said that data on its service can not be accessed by Beijing, said it had not been told or contacted by either institution ahead of their decisions.
"So we are really operating under a cloud. And the lack of transparency and the lack of due process. Quite frankly one would expect, you know, some sort of engagement on this matter," Caroline Greer, TikTok's director of public policy and government relations, told Reuters.
She said she cold not respond to the bodies' cybersecurity concerns because they had not spelled them out.
The European Commission did not immediately respond to a request for comment on TikTok's statement.
Greer said TikTok CEO Shou Zi Chew, who met EU industry chief Thierry Breton and other commissioners in Brussels in January, was "concerned and a little puzzled".
"He has always been very available, you know, responding to the Commission ... We have reached out for a meeting in whatever shape or form they would like that to happen."
Other EU institutions should do their own research before making decisions on the app, Greer said.
TikTok is banned on U.S. Senate employees' government-owned devices and also in India. The European Parliament has not taken such a step.
(Reporting by Foo Yun Chee; Editing by Andrew Heavens)
By Foo Yun Chee
