The open cast mine is meant to supply coal to a new 300 megawatt (MW) power plant set to be built by independent power producers as part of Botswana's plans to be self-sufficient in power generation by 2020.
Developer Morupule Coal Mine (MCM) said in a statement that six of the 166 farmers affected had declined to accept proposed compensation but that the company was trying to resolve the issue.
The company said about 200 million pula ($20 million) would be lost monthly due to the delay, and half of the losses were being shouldered by the government.
The government has been forced to import electricity to plug a power deficit. The country has one operating power station with a generating capacity of 600 MW but the plant has broken down often since its launch in 2012, prompting imports from South Africa.
The construction of a second, 300 MW power plant has been delayed by a dispute with the contractors over a sovereign guarantee.