The United Nations Environment Programme (UNEP) said studies had shown old sites and also operational mines might be contaminating water supplies and the air.
"There are tens of such sites in each country, so it could add up to hundreds in the region," Philip Peck, an UNEP consultant, told Reuters from the Romanian city of Cluj where UNEP is holding a seminar on mining and the environment.
"Most of these sites are likely to have very serious consequences on the environment," he said.
Peck said water must be prevented from going in and out the abandoned mines and large mine waste deposits should be properly disposed of.
Over a third of around 150 old mining sites in Albania, Bosnia Herzegovina, Macedonia, Serbia and Montenegro and Kosovo that were used to extract zinc, copper, bauxite, silver, gold and cadminum might pose serious risks to human health, according to a UNEP study.
Some operational sites might also pose a threat, one example being a major cyanide spill from a gold mine in Romania five years ago, which polluted the river Tisza in neighbouring Hungary and the Danube.