The bench of Justice Md. Ashraful Kamal and Justice Razik-Al-Jalil passed the order after hearing a writ petition.
According to the directive, all due revenues, in the form of value added tax (VAT)or any other taxes for the past five years should be collected.
The HC also ordered the authorities to submit separate reports on progress towards implementing the directive every six months.
The directive will be a continual Mandamus, HC said, that is an order from a court to any government, subordinate court, corporation, or public authority, to do (or forbear from doing) some specific act which that body is obliged under law to do.
In this case, the order is incumbent upon NBR, Bangladesh Bank, BTRC, as well as other government agencies.
Any citizen of the country will be able to move prayer before the HC if the directive is violated, HC said.
Six Supreme Court lawyers, including Mohammad Humayun Kabir Pallab, Mohammad Kauser and Md Sajjadul Islam in 2018 filed the writ petition seeking necessary directives over the matter.
The internet-based firms, particularly the global giants such as Facebook and Google, have grown notorious for avoiding taxes in the countries they operate and earn revenue themselves.