The surprise nomination will put Shmatko, a nuclear reactor salesman with a military education and no experience in oil or gas, at the helm of Russia's energy industry, the world's largest natural gas producer and second largest oil exporter.
Shmatko, 42, has been in the spotlight in recent years over his company's construction of a nuclear power plant at Bushehr, on the Gulf coast in southwestern Iran.
Under a $1 billion construction contract, Russia has already made deliveries of nuclear fuel to the plant, despite U.S. and European concerns over Iran's uranium enrichment program, which some fear could be used to produce a nuclear bomb.
Aside from entrusting him to implement oil and gas policy, the post of energy minister will also make Shmatko one of the key regulators of the electricity sector, which is in the process of implementing sweeping free-market reforms.
Shmatko has headed Atomstroiexport since 2005, and since January of this year he has also served as deputy director of AtomEnergoProm, the state giant that includes all of Russia's civilian nuclear assets.
It was not immediately clear whether Shmatko would retain these positions after taking on his new role.He took up his post at the reactor construction firm just after graduating in 2004 from a top military academy, where he specialized in "the defence and security of the Russian Federation," according to his official biography.
In the late 1980s, Shmatko worked on Soviet nuclear submarines in the Northern Fleet, the biography posted on Atomstroiexport's Web site said.
The post of energy minister was created in the current shake-up of the government, which saw the industry and energy ministry split into two on order of the Prime Minister Vladimir Putin, who took his position last week.
Viktor Khristenko, the former minister of industry and energy, will now be the minister of industry and trade, while Shmatko will takes over the energy portfolio.
While serving in his previous role, Khristenko also took positions on the board of some of Russia's largest energy companies, including former electricity monopoly UES, oil pipeline monopoly Transneft, and natural gas export monopoly Gazprom.
In the wake of the government re-shuffle, analysts are also expecting personnel changes in the upper ranks of state-controlled companies, where government ministers traditionally get a seat on the board.