The nature of the breakdown was not immediately clear. It was the first time the navy indicated it had been aware of a problem.
"The vessel surfaced and it reported a breakdown. It was therefore asked to change course and go to Mar del Plata," said Gabriel Galeazzi, the head of the naval base in the northeastern city, located 400 kilometers (250 miles) south of Buenos Aires.
Enrique Balbi, a spokesman for the navy, meanwhile told a press conference in the capital that seven signals received by naval bases over the weekend were not attempted distress calls from the submarine, as had been previously hoped.
"We've received the report from the company that analyzed the signals -- the seven attempted calls did not come from the submarine's satellite phone," he said, adding: "We have still been unable to contact them."
The ARA San Juan, a German-built diesel-electric sub, made its last contact on Wednesday.
A multinational air and sea search is under way with help from countries including Brazil, Britain, Chile, the United States and Uruguay.
The CNN news channel reported Monday that Argentina's navy had detected noises that could be distress signals from the crew of the missing submarine.
The noises sounded like tools being banged on the hull of a submarine, CNN cited a senior official in the US navy familiar with the search as saying.
False hope?
Monday's revelations were a blow to relatives of sailors aboard the sub, around 100 of whom are being housed at the Mar del Plata naval base as they await news of the crew.
"They have a lot of hope. The hours go by and the worry rate goes up. The best tranquilizer is accurate information," said Enrique Stein, a member of a psychological support cell set up for the families.
"We don't know anything. We are waiting with a great deal of anxiety," said Andrea Ali, wife of Franco Ali, an electrician aboard the San Juan.
The submarine's fate has gripped the nation, and President Mauricio Macri visited the relatives and prayed with them on Monday. Macri was briefed on the search by Vice Admiral Miguel Angel Mascolo during his visit to the base.
The navy said Saturday it had received seven calls that day but they did not lock in, an announcement that left many cautiously optimistic they were signs of life from the vessel's crew.
On Sunday, a flag was unfurled at the naval base that read: "Be strong Argentina, We trust in God, We wait for you."
At the Vatican, Argentine-born Pope Francis said he offered "his fervent prayer" for the safety of the submarine sailors.
Multinational rescue efforts
Search efforts meanwhile have been hampered by inclement weather, including a powerful storm that has whipped up waves reaching seven meters (23 feet) in height.
Rescuers are focusing on an ocean patch about 300 kilometers in diameter, radiating from the last point of contact.
US Southern Command has deployed a Navy P-8A Poseidon patrol and reconnaissance plane with a crew of 21, along with a NASA P-3 research aircraft, and other equipment and personnel.
The US Navy has deployed two unmanned underwater vehicles that use a sonar system to create an image of large sections of the sea floor.
Britain's Royal Navy said it had sent the HMS Protector, an Antarctic patrol ship.
The TR-1700 class submarine had been returning from a routine mission to Ushuaia, near the southernmost tip of South America, to Mar del Plata.
It is one of three submarines in the Argentine fleet.
Sixty-five meters long and seven meters wide, it was built by Germany's Thyssen Nordseewerke and launched in 1983.
It underwent a refit between 2007 and 2014 to extend its use by about 30 years.
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