According to AIM, thieves hacked through the ceiling of the storage room to gain access.
It said a team comprising members of the Criminal Investigation Services (SERNIC) and ANAC officials has been created to investigate the case.
The disappeared ivory consisted of 85 pairs of tusks held by the Niassa Provincial Forest and Wildlife Services.
The authorities attribute the disappearance to a succession of unsolved robberies that have occurred since April 2016.
Elephant tasks and rhinoceros horns, lion and leopard teeth, pelts and claws are among the trophies sought by the international traffic in animal parts in Mozambique.
Elephants have been worst affected and in the last five years amid reports that the population in the country’s conservation areas has shrunk from about 20,000 to half that number.
Two years ago, Mozambique burned 2.5 tonnes of seized ivory and rhino horn as part of a campaign to end an illicit trade that was fuelling a wave of big-animal poaching in Africa.
Neighboring South Africa lost a record 1,125 rhinos last year, up 20 percent from 2013, as poachers looked to meet surging consumption in Vietnam, where the animal's horn is coveted as a key ingredient in traditional medicines.