The train was travelling from the mine in Tete province on Wednesday, destined for the export terminal at the port of Beira, in Sofala province.
The train driver was injured during the attack.
Only a day before, assistant national director for defence policy Manuel Mazuze told local media that armed attacks in Sofala province were averaging two a day.
The majority of the attacks were attributed to the country’s opposition party, Renamo.
A press release by Vale Mozambique stated the attack happened at 9pm local time.
It noted that the locomotive had been hit by a number of shots and reported just one casualty, the driver, who was shot in the leg.
His condition was said to be stable.
The country’s opposition party Renamo denied any involvement in the attack.
It is rumoured the attacks were possibly staged by a “counter- intelligence force” to damage Renamo’s image.
It has been proposed that such an operation could have been stimulated by rumours that Vale Mozambique had been paying Renamo not to attack its trains.
Despite the incident, Vale plans to spend just over $US2 billion ($AU2.13billion) through 2015 to construct a second open pit at Moatize which will increase annual production to 11 million tonnes.
The company also aims to finish its more than $US4.4 billion transport corridor to the Nacala port by the end of this year.