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The 40-year-old Kosovo A plant, considered one of the worst polluters in Europe, was shut down following the blast that was heard in the capital, Pristina, some 10km away.
The explosion threatened electricity supplies in a country already plagued by blackouts. Power imports were increased to cover demand.
"We have found two bodies," Edmond Nulleshi, a manager at the Kosovo's Energy Corporation (KEK), told Reuters.
Local television footage showed soldiers rescuing a worker who had been trapped in the building for more than five hours.
An investigation has been launched into the incident.
The Yugoslav-era plant and the larger Kosovo B account for 90 percent of electricity generation in the Balkan country, which still suffers chronic power shortages 15 years after breaking free of Serbia in a 1998-99 war during the collapse of federal Yugoslavia.
Costly plans to build a new plant that would allow Kosovo A to be closed for good have been delayed for years, with some critics blaming the government for toying with the rules of the tender.
Kosovo's main political parties cancelled final campaign rallies planned for Friday before a parliamentary election on Sunday.
Health Minister Ferid Agani told reporters that 13 people had been treated for injuries that he said were not life-threatening.
Economy Minister Fadil Ismajli, whose ministry covers the energy sector, told Reuters that the 345 megawatt (MW) Kosovo A had been shut down. The blast occurred in the electrolysis unit, not the generators.
Kosovo's energy distribution and supply company, KEDS, said it had imported 250 megawatt-hours (MWh) of electricity to cover demand. Spokesman Guri Shkodra told Reuters it was unclear when the plant would be back online.
Albania's energy ministry said it has started sending 50 MW of electricity out of 200 MW per day demanded by Kosovo to help it cope with shortages.
It said Albania's power utility KESH and power distributor OST and their counterparts in Kosovo were trying secure interconnection capacities to meet the need for the requested power.
Kosovo is connected to Albania via a 220 kV line. Work is under way to build a more powerful 400 kV line.
Last year, international donors pledged 154 million euros ($209.67 million) to help close down Kosovo A, improve energy efficiency and diversify energy sources in the landlocked Balkan country, one of Europe's poorest.
The European Commission says the cost to decommission the plant, which produces a quarter of electricity consumed in Kosovo, is seen at 60 million euros, and that the commission is ready to ask member states to fund the project. ($1 = 0.7345 euros) (Additional reporting by Maja Zuvela in Sarajevo and Benet Koleka in Tirana; Writing by Matt Robinson; Editing by Angus MacSwan and David Evans)