The site at Ketzin, outside Berlin, is part of a European project dubbed CO2SINK which aims to test whether capturing and storing carbon dioxide in subterranean rock is a viable way of fighting global warming, the GFZ centre in Potsdam said.
It will pump up 60,000 tonnes of the greenhouse gas into porous, salt water-filled rock at depths of more than 600 metres (656 yards) over the next two years, the centre said.
The first injection of gas below the surface was due to take place later on Monday.
Reinhard Huettl, the science director of the institute, said storing carbon dioxide underground could slow down global warming and thereby buy scientists extra time to develop alternative energy sources.
"The storage of the greenhouse gas carbon dioxide is an option to win time in the development and introduction of carbon dioxide-reduced energy technology," he said.
Huettl said the site will become a "unique worldwide laboratory" to study the success of the world's main global warming gas.
Some environmental groups have expressed reservations about capturing carbon emissions produced by industry to store it below ground, with Greenpeace saying it posed the risk of highly toxic leaks.