The southern African country said it had granted two companies permission to explore for underground gas in the Kalahari National Park, raising concerns about the environmental impact on the world's second-largest game reserve.
The government of the desert-covered country also denied charges from a governance group that it was secretly allowing the controversial process of "fracking" or hydraulic fracturing.
Gaborone issued prospecting licences for coal bed methane within the Central Kalahari Game Reserve to Australia's Tlou Energy and to African Coal and Gas Corp, the environment and mineral ministries said in a joint statement.
Coal bed methane is natural gas extracted from coal beds.
"While concessions for energy prospecting have indeed been granted over wide areas of the country, there are currently no mining licences for gas extraction ... And thus no commercial production involving so-called fracking," the ministries said.
Fracking is a technique used to extract underground shale gas by digging deep wells and pumping in large amounts of water mixed with chemicals under high pressure to crack the rock.
Critics of the process say it could contaminate water sources.
The Open Society Initiative for Southern Africa, a governance group, has said Botswana's government has been quietly pushing ahead with plans to produce natural gas and that drilling and fracking are already under way.