Argentina's navy says its ARA San Juan submarine, which has been missing since Wednesday, reported a mechanical breakdown in its last communication.
The submarine, with 44 crew on board, disappeared 430km (270 miles) off the Argentine coast.
"The vessel surfaced and it reported a breakdown," naval commander Gabriel Galeazzi said.
Argentina's navy said a "noise" picked up by sonar on Monday during the search did not come from the vessel.
It is the second false alarm in the hunt for the submarine.
Capt Galeazzi, who heads the naval base in Mar del Plata, south of Buenos Aires, said that the fault reported earlier related to a "short circuit" in the sub's batteries.
The brother of a crew member earlier told local media that in a message before communications were lost his sibling had mentioned that the vessel was having problems with its batteries.
This is the first time that an official has mentioned the sub encountering mechanical problems.
However Capt Galeazzi said that mechanical problems were not uncommon and rarely posed a risk.
"A warship has a lot of backup systems, to allow it to move from one to another when there is a breakdown," he said.
The naval commander said that the submarine had been asked to cut short its mission, which was originally due to last until Monday, and go directly to Mar del Plata.
According to local media, the captain of the ARA San Juan contacted the naval base again after reporting the mechanical problem.
In the message, he reportedly said the sub was heading towards Mar del Plata with all 44 crew members in perfect health.
Signals not from sub
The navy also announced on Monday that seven signals picked up at the weekend were not from the missing submarine's satellite phone.
The failed calls, lasting between four and 36 seconds, had been received on Saturday. They had raised hopes that the crew members were alive.