Vice-minister for international affairs in the Ministry of Economy, Trade and Industry, Tadakatsu Sano, told the Australian Financial Review the new surcharge did not amount to an environmental tax and was not designed to be punitive.
"We're not trying to discourage the usage of energy, rather we'd like to encourage the rational use of energy," Sano told the paper.
"And at the same time we'd like to encourage alternative energy, which is less damaging to the global environment."
Japan already taxes imports of petroleum, natural gas and other energy sources, but not coal.
Sano was quoted as saying details of the tax are still undecided, but the government intended to have it ready for the new financial year on April 1. In the meantime the ministry will consult energy consumers, and Sano indicated the actual start date may be delayed while "documentation" is prepared.
Any new tax is likely to affect Australia's $5 billion worth of annual thermal and coking coal sales to Japan.
Australia is the world's largest exporter of coal and Japan the largest coal buyer.