Interior ministry spokesman Shota Utiashvili said there had been several explosions near an abandoned Georgian military base where the Russian troops, on leaving Gori, had left a stockpile of munitions taken from the Georgian army.
Black smoke and flames rise from the train
He suggested the stockpile or the train track could have been mined by the Russian forces. He said there had been no casualties.
Georgian authorities had been hoping to help thousands of refugees return to Gori on Sunday having carried out a mine-sweeping operation in the town, which lies close to the border with the breakaway province of South Ossetia.
Georgia's Prime Minister Lado Gurgenidze said it would be important to see the extent of the damage, once the fire had been extinguished.
"The railway is vital, not just for the Georgian economy but for the economies of neighbouring countries," he said.
The track runs through the capital Tbilisi before splitting and running to the Black Sea ports of Poti and Batumi and south-west towards the Turkish border.
One of the train's wagons was marked Azpetrol - a company based in Baku, Azerbaijan.
President Sarkozy called a special summit of EU leaders to discuss the Georgian crisis, to be held in Brussels on 1 September.
His office said the summit, arranged at the request of various European countries, would discuss the future of EU relations with Russia as well as aid for Georgia.
Russia's four-day war with Georgia erupted after Tbilisi tried to retake South Ossetia - which broke away in 1992 and was supported by Moscow - in a surprise offensive on 7 August. The offensive followed a series of clashes between Georgian and South Ossetian forces.
No more use of force
Stop all military actions for good
Free access to humanitarian aid
Georgian troops return to their places of permanent deployment
Russian troops to return to pre-conflict positions but Russian peacekeepers may take unspecified "additional security measures"
International talks about security in South Ossetia and Abkhazia
The conflict left hundreds of people dead and created tens of thousands of refugees. Many have been returning to their damaged or destroyed homes since the Russian withdrawal.
The UN's refugee agency UNHCR reported this week that, according to Russian estimates, more than 30,000 people from South Ossetia had fled to North Ossetia. Another 128,000 were estimated to have been displaced within Georgia.
International aid agencies are working on the ground and the US has already delivered some aid by military cargo plane.
The destroyer USS McFaul is reported to be carrying supplies such as blankets, hygiene kits and baby food. The supplies will be unloaded by a floating crane as the port is too shallow for the ship to dock.
Two more US ships are due to arrive later this week.
The BBC's Gabriel Gatehouse, aboard the American warship, said that apart from delivering aid, the arrival of US naval personnel is undoubtedly intended to send a signal to the Russians - that America is serious about its support for Georgia.
But, he adds, the prospect of US and Russian armed forces actually meeting on Georgian soil is one that both sides seem keen to avoid.
Batumi is not a natural harbour for a naval vessel the size of the USS McFaul to dock, but Russian forces have been fortifying their positions at the key port of Poti, further up the coast.
On Saturday, Mr Sarkozy welcomed the withdrawal of Russian forces so far, but urged Moscow to pull its troops back from Poti and Senaki, which is the site of Georgia's main air base.
Russia says it has a duty and a right to keep its forces in a buffer zone around the breakaway territories of Abkhazia and South Ossetia - though it acknowledges that Poti falls well outside that zone.
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