Argentina's navy says it has launched an air and sea operation to restore contact with a submarine off the country's southern coast.

The navy said on Twitter on Friday that the ARA San Juan was heading from Ushuaia, in the country's south, to a base in Mar del Plata, about 400km south of the capital, Buenos Aires.

Enrique Balbi, navy spokesman, said the last contact of the vessel with the command was on Wednesday morning.

The submarine has at least 40 crew members on board, according to local media reports.

Speaking of a "communication failure", the navy said the submarine is not considered lost, while Balbi denied a report that there may have been a fire on board.

"I don't want to dramatise the issue," he said.

"We're lacking communication and don't know what happened."

'We are totally desperate'

A sister of a crew member working in the kitchen of the submarine said that no one from the navy had communicated with the family of the officer.

"We do not know anything about our relatives, we are totally desperate," said the crying sister, identified by popular Argentine daily Clarin as Cristina.

According to Clarin, the ARA San Juan is a diesel-electric submarine that was manufactured in Germany.

It has been part of Argentine's navy since 1985.