Satellite calls detected over the weekend during a search-and-rescue operation did not come from vessel, dashing hopes the crew were trying to make contact.
Waves up to 20-feet in the area where the sub went missing, about 260 miles from the Argentine coast, were complicating the global search effort, Adm. Gabriel Gonzalez, commander of the base, was quoted by The Associated Press as saying.
Its last contact with navy command was on Wednesday morning.
The diesel-electric ARA San Juan was returning to its base south of Buenos Aires after a routine mission to Ushuaia, near the southern tip of South America, on Wednesday.
The satellite call attempts were registered between 9am and 3pm on Saturday, lasting between four and 36 seconds, but there was no voice contact.
"The calls are being analyzed, but we do not have clear evidence that they came from that unit", said Gabriel Gonzales, who is in charge of the base where the submarine was slated to arrive Sunday, according to state-run news agency Télam.
Argentine President Mauricio Macri met with family members at the base as they waited anxiously for news about their loved ones.
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The Argentine military has also been working with a United States company that specializes in satellite communication to determine the location of the submarine.
USA satellite company Iridium had earlier said that the submarine carried one of its satellite phones on board.
Dozens of aircraft and ships, including a British polar exploration vessel, have joined in search efforts that have attracted the world's attention.
Vessels from Argentina, the US, Great Britain, Chile, and Brazil have joined other vessels and aircraft looking for the submarine. The location of the noise coincides with the route the submarine would have taken on the way to its home port in Mar del Plata. "It was therefore asked to change course and go to Mar del Plata".
Among those on board is Argentina's first female submarine officer, 35-year-old weapons officer Eliana Krawczyk.
The calls "did not correspond to the satellite phone of the submarine San Juan", Balbi said. Built in Germany by Nordseewerke, it underwent mid-life maintenance in 2008 in Argentina.
SOUTHCOM directed the deployment of the P-8A aircraft, underwater rescue teams and personnel to assist Argentina as support, the country request for global assistance to locate the missing submarine and crew.