Residents of the region want the government to redistribute taxes paid by the region's Southern Copper Corporation, the country's largest copper producer.
Clashes erupted on Monday after police, armed with tear gas but vastly outnumbered, were overpowered and seized by club-wielding protesters as they attempted to break the blockade of a bridge.
In the past week residents of Moquegua have occupied roads, including Peru's main highway to Chile, and severed access to a mine and smelter belonging to Southern Copper.
The blockade has also cut road links to Tacna, Peru's southernmost province, forcing the government to send food and fuel by sea to replenish supplies.
Analysts have said that Peru, a leading global exporter of minerals, could see other regions holding protests in a bid to reap what they see as their fair share of mining taxes.
Social unrest is common in Peru's mining regions, where residents accuse large mining companies of reaping large profits while polluting the environment and offering little benefit to locals.