The boat has enough supplies to last several days and is likely to continue its journey in spite of the communications issue.
Local media reported that contact with the San Juan was lost after a fire affected the submarine's radio equipment.
From 2007 to 2014, the submarine underwent repairs to extend its use for 30 more years, which included fix of the 960 elements of its batteries, where officials say a failure could have originated. "We're lacking communication and don't know what happened", he said.
"The last communication was on Wednesday", Balbi said.
Relatives of some of the crew members are at the base awaiting word of the search.
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Pyongyang maintains a diplomatic presence in Singapore, with an embassy in its financial district. North Koreans have been required to get a visa to enter Singapore since October previous year .
It was constructed in Germany in 1985 and joined the Argentine Navy a year later.
The TR-1700 submarine is run with diesel-electric propulsion and authorities said its objective was to carry out surveillance exercises in the economic zone around Puerto Madryn. On its current mission, it has 44 crew members on board, including the first female submariner in the country's history.
The sub was travelling from a naval base at Ushuaia in the far south to Mar del Plata, around 200 miles south of Buenos Aires, when it vanished.
According to Naval Spokesperson Enrique Balbi, the navy and air force are conducting extensive searches in the area where the submarine was last seen.
The ARA San Juan is one of Argentina's three submarines and has four, 16-cylinder, 1,200 Kw diesel engines.