Two suitcases filled with flammable material which investigators believe may have been explosive devices were found at the scene, said V.N. Mathur, general manager of the Northern Railway. He said one was found inside a burned coach and the other on the railroad track.
Speaking to reporters at the scene, India's junior railway minister, R. Velu, said: "We have 64 bodies."
Residents living near the tracks rushed to scene with buckets of water soon after the fire broke out and the blaze was eventually extinguished when fire trucks arrived.
The fire engulfed two cars of the Samjhauta Express, one of two train links between rivals India and Pakistan. It broke out just before the train reached the station in the village of Deewana, about 50 miles north of New Delhi.
Mathur told reporters 64 bodies have been recovered from the burned-out cars and at least 30 passengers burned and injured in the blaze have been hospitalized in the nearby town of Panipat.
The train was traveling from New Delhi to Atari, the last railroad station before the border with Pakistan.
The train links are one of the most visible results of the peace process under way between nuclear-armed India and Pakistan, and one of the easiest ways to travel between the two countries.
Within hours of the fire, authorities detached the burned cars and the rest of the train continued on to the India-Pakistan border.