Cambodian officials have given no explanation for the premier's decision to remove Chea Sophara, who was reportedly outside Phnom Penh when angry mobs ransacked and burned the Thai embassy and prominent Thai businesses.
But Mr Chea Sophara, who sought to beautify Cambodia's dilapidated capital in recent years, had expressed concern about protecting Khmer culture against an onslaught of foreign influences, particularly Thai.
Thai security officials have suggested that such sentiments may have helped fuel resentment against Thais. Mr Chea Sophara, who once enjoyed close ties with the premier, has now been appointed Cambodia's ambassador to Burma.
The political exile of the well-liked governor comes amid slow improvements in Cambodia's strained relations with Bangkok, which evacuated all Thai citizens from Phnom Penh after the violence.
Although relations have yet to be fully normalised, Thailand on Monday sent several diplomats - led by a chargé d'affaires - to re- establish a presence in Phnom Penh, after Mr Hun Sen personally guaranteed the diplomats' safety.
Thailand last weekend also eased controls along its border with Cambodia to allow the resumption of trade, ending a nine-day closure that had brought severe hardship to Cambodians in border areas, which depend on Thailand for food and other essentials.
Cambodia has pledged to compensate Thailand for the damages to Thai property and to identify and punish those responsible for the attacks, which has helped assuage Bangkok's anger.
Authorities took control of Beehive Radio, Cambodia's only independent radio station, after charging Mom Sonando, the station's chief broadcaster, with inciting the riots. Rights groups say the radio personality has been unfairly blamed for an inflammatory comment made on air by someone who called in to his programme.