The vessel went out of contact while en route from the islands of Argentina's Tierra del Fuego to the Armada Argentina's northern base at Mar del Plata.
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 onboard.
Commander Galeazzi said it was normal for submarines to suffer system malfunctions.
According to national Argentinian newspaper La Nacion, it was subjected to years of complex fix and engineering work in 2008, which the country's navy believed would extend its life by 30 years.
Over the weekend, Argentina's Defense Ministry reported receiving seven "failed satellite calls" that officials thought might be coming from the missing submarine. But the weather continues to pose significant challenges to a rescue attempt as well as the search, and it will be hard to dock the Submarine Rescue Chamber to the San Juan's deck if the sub is on its side or at an angle on the bottom. "I also pray for the men of the crew of the Argentinian military submarine which is missing", the pontiff said. He said similar conditions were expected for the next two days.
Dozens of aircraft and ships, including a British polar exploration vessel, have joined in search efforts that have attracted the world's attention.
All terrestrial communications stations along the Argentine coast have been ordered to search for communications and listen to all possible frequencies of transmission by the submarine to try and make contact with the vessel.
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Among the 44 crew members is Argentina's first female submarine officer, 35-year-old Eliana Krawczyk.
If the sub is bobbing adrift on the surface and the hatch is open, it will have an available air supply and enough food for about 30 days, he said.
The ARA San Juan was inaugurated in 1983, making it the newest of the three submarines in the navy's fleet.
The dramatic search has captivated the nation of 44 million, which recently mourned the loss of five citizens killed when a truck driver plowed through a bicycle path in New York City. However, it would not be unusual for storms to cause delays, Balbi said.
The government on Sunday said it could not confirm that the attempts had come from the ARA San Juan.
At the Vatican, Pope Francis, a native of Argentina, said he was sending "fervent prayers" for the crew.