Rio Tinto suspended coal exports from northwest Mozambique after the opposition Renamo party threatened to disrupt a railway line in Tete province, which carries coal to the coast.
Recently, former guerrillas took up arms, more than 20 years after the end of a civil war.
Rio Tinto said it had "paused" its operations on the rail line, but production continues at its Benga mine.
Sena is the only railway line leading from the Tete coal fields to the Indian Ocean port of Beira.
"As for Rio Tinto's goods trains, the company decided to suspend them," Tete provincial governor Rachid Gogo told Radio Mozambique on Wednesday.
The railway's main user is Vale of Brazil, which is investing $US4 billion in its coal mine operations in Tete.
In a statement, Vale said that it continues to use the Sena line, but has heightened security.
Renamo is a former guerrilla movement which waged war against the ruling Frelimo party from 1975 - 1992.
Renamo threatened to renew armed hostilities last year, in an attempt to win more concessions from the Frelimo government at a time of economic boom in Mozambique.
Last week, Renamo announced a specific threat to public roads and the Sena railway.