At least 20 people were injured in fresh clashes with police on Sunday after protesters gathered near the offices of Asia Energy in Phulbari, where the mine is being developed.
The demonstrators demanded its immediate closure.
Local residents and rights groups say the mine would displace hundreds of families and damage the environment.
Police also evicted a group of protesters who blocked a road bridge linking the northern districts with the capital Dhaka disrupting traffic.
In the capital, students of Dhaka University staged demonstrations demanding the resignation of the government's energy adviser, Mahmudur Rahman, and state minister for home affairs, Lutfuzzaman Babar.
Students have called for a strike in educational institutions across the country on Monday to protest against the killings of the protesters.
Gary Lye, chief executive of Asia Energy Corporation (Bangladesh), issued a statement on Saturday denying that the Phulbari project would harm the environment and said it would benefit local people.
In another statement on Sunday, Lye said that Asia Energy deeply regretted what had happened and sent its sympathies to the families of the dead and injured.
Rahman said: "This incident has sent the wrong message to foreign investors, which we cannot afford at all when we are struggling hard to woo more and more investment."