Environmental activists say he was a major impediment to stopping illegal logging in the province.
Criticism has been particularly harsh after a report was released last year by the U.N. Special Rapporteur for Trafficking in Persons.
A third victim dropped her complaint after receiving around $1,000.
They have demanded Phanimex build two more buildings to house ousted residents and pay compensation if around $1,000 per family.
Chhouk Bandith's deputy, Deb Saroeun, will replace him on Friday.
Deputy police chief Keo Kong and Huot Samay and commune chief of Chrak Matess denied they have been involved in negotiations.
Chhouk Bandith is accused of firing into a group of some 1,000 protesters who had gathered to demand higher wages.
Chhoung Chu Ngy is accused of helping a deputy commune chief for the Sam Rainsy Party, leave detention at the Kandal court last year.
Witnesses said the suspect stepped out of his car, pulled out a hand gun and opened fire on a crowd of over 1,000 protesters.
Villagers complained that the new location lacks enough clean water, electricity, roads, schools and access to health care.
At least 50 people, whose houses were bulldozed early January, said their names are not in the new housing list.
Lt. Gen. Chhoeun Chanthan was found guilty for breach of confidence, distribution and selling of weapons and mismanagement.