Global Witness, in a report, highlights a 2008 copper contract and a 2010 gold contract, the two largest mining deals signed in Afghanistan.
Global Witness said it had "serious concerns" about the lack of transparency in both contracts, noting negotiations left out members of the local communities likely affected by mining development.
"Afghanistan's mineral sector will be critical in generating much needed income to fill the funding-gap post-transition but only if managed properly," Global Witness campaigner Juman Kubba said in a statement.
U.S. defense officials estimated in 2010 that there could be as much as $1 trillion worth of iron, copper, cobalt, gold and lithium in Afghanistan. Last year, a consortium of Indian mining companies and Canada's Kilo Goldmines secured rights to explore mineral deposits in Afghanistan.
Afghan officials said production of iron ore deposits in Bamyan province could begin in 2015.
Global Witness, an advocacy group working to decouple conflict from natural resources, said it was calling on Afghan officials to publish its mining contracts ahead of a donor's conference in July.