"I will strive to create a better society and a society which can hand down a wonderful environment to next generations," Koizumi said as he switched on the system.
The eco-friendly system, made up of two units, can generate a total of two kilowatts of electricity and at the same time serve as boilers while limiting its carbon dioxide emissions.
The premier's new residence, where Koizumi is scheduled to move in a few months time, also features wind-powered generators to emphasise his government's drive for environmental protection.
In the system, electricity is generated through chemical reactions of hydrogen taken from home gas and oxygen from the air, with heat produced through the reactions.
Japan -- home of the Kyoto Protocol, the global environmental treaty which took effect in February -- has been promoting eco-friendly technology which is the main theme of the ongoing World Exposition in central Aichi province.
Koizumi has pledged to take off his jacket and tie this summer to save on the energy needed for air conditioning.
One of the units at the prime minister's residence was developed by Matsushita Electric Industrial Co. and the other by a subsidiary of engineering firm Ebara Corp., Kyodo News said.
Both units have a tank capable of holding 200 liters of water at 60 Celsius (140 Fahrenheit). Tokyo Gas Co. supplies gas fuel to the units.
Tokyo Gas has been accepting applications for the fuel cell systems from ordinary household users since February. It plans to install 200 units of the new system within its supply area by next March.
A 10-year contract to use the new power system will cost a household 1 million yen (9,200 dollars), according to Tokyo Gas.
Fuel cells, using hydrogen or alternative fuels such as methanol, are widely expected to replace existing lithium-ion batteries for mobile devices.