Germany, which has committed to phase out nuclear power, emitted the equivalent of around 931 million tonnes of carbon dioxide in 2012, or 14 million tonnes more than a year earlier, the agency said on Monday.
"Greenhouse gas emissions in Germany increased slightly in 2012 by 1.6 percent," it said in a written statement.
"More coal was burned to generate electricity and more gas was used to heat homes, due to the weather," it added. "The development of renewable energies abated the emissions' increase however."
After the 2011 Fukushima disaster in Japan, Germany embarked on an ambitious "energy revolution," deciding to phase out its nuclear power plants by the end of 2022 and bolster renewable sources of energy such as solar and wind power.
But concerns have mounted that this would entail a sharp rise in electricity prices amid difficulties in building a network able to transmit energy from the North Sea coast to the energy-hungry south of the country.
The agency's president Jochen Flasbarth said fears that the nuclear exit would spark far greater greenhouse gas emissions had not happened "because, above all, the further development of renewable energies has countered it."
"However, the trend of again converting more coal into electricity worries me," he added in the statement.
Germany said that despite the slight increase in emissions in 2012, it had more than met the targets agreed under the Kyoto Protocol, with its greenhouse gas emissions having fallen by 25.5 percent compared to 1990.