"Several metres of the railway line are destroyed and repair works are under way and it will be reopened very soon," Gogokhia said.
The explosion took place near the village of Ingiri, about 300km from the capital Tbilisi, on one of the main routes for passenger and cargo trains.
"I think it's a pure terrorist attack because some explosives and a clock mechanism were used"
Zurab Gogokhia, chief of Georgian Railways
But an interior ministry official said the route was not one of those used to ship Caspian oil from Azerbaijan to Georgia's Black Sea coast.
The blast comes just days after Georgia's breakaway region of South Ossetia held elections.
Georgia attempted to retake South Ossetia last year, sparking a five-day war with Russia, which backs the province.
Moscow subsequently recognised both South Ossetia and Georgia's second breakaway region of Abkhazia as independent countries.
The site of the explosion was close to the de facto border with Abkhazia, but there was no immediate evidence of any separatist involvement.