The San Juan, which has a crew of 44, was last heard heard from on Wednesday before it went missing in the Atlantic Ocean.
Recent bad weather in the region has made the search more hard for aircraft and ships; the Patagonia Coast is known for bad storms.
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.
Waves up to 20-feet in the area where the sub went missing, about 260 miles from the Argentine coast, were complicating the worldwide search effort, Adm. Gabriel Gonzalez, commander of the base, was quoted by The Associated Press as saying. The Bluefin 12D is capable of conducting search operations at 3 knots (3.5 mph) at a maximum depth of nearly 5,000 feet for 30 hours, while the Iver 580s can operate at a depth of 325 feet, traveling at 2.5 knots (2.8 mph) for up to 14 hours.
Crew members' relatives gathered at the naval base, waiting for news.
The British polar ice patrol ship HMS Protector, equipped with sonar equipment, is also providing assistance.
"We are not discounting any hypothesis", Balbi said, adding that possibilities to explain the submarine's disappearance include "a problem with communications" or with its power system.
All land communications bases along the coast were ordered to scan for any follow-up signals, as family members of the missing waited nervously in the coastal city of Mar del Plata.
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Fears are growing for an Argentine submarine with a 44-member crew which has not been heard from since Wednesday.
The submarine was originally scheduled to arrive Monday to the base in Mar del Plata, about 250 miles (400 kilometers) southeast of Buenos Aires. "Thank God", he said.
One of those on board is Argentine Eliana Krawczyk - who became the first female South American submariner.
The navy has not ruled out any hypothesis.
The government on Sunday said it could not confirm that the attempts had come from the ARA San Juan. Built in Germany, it underwent maintenance in 2008 in Argentina.
"We are analyzing more closely to reliably determine that they weren't calls coming from the submarine", said Adm. Gabriel Gonzalez, chief of Mar del Plata Naval Base, in a statement to press this morning.
"It's dependent upon the last time they actually recharged their batteries, how long ago they refreshed the air, what's inside the submarine", former U.S. Navy diver and submariner William Craig Reed told CNN.