Mr Balbi said: "We've received the report from the company that analysed the signals - the seven attempted calls did not come from the submarine's satellite phone".
Navy spokesman Enrique Balbi says Monday that a US aircraft was sent to check an area where the noise was heard by two Argentine Navy ships.
The United States assisted in the search for a missing Argentine submarine, reported by the media.
"This phase of search and rescue is critical", Balbi said.
It is one of three submarines in the Argentine fleet.
The plane dropped sonar buoys into the sea to record the noises. However, it would not be unusual for storms to cause delays, Balbi said. All these will beef up search effort, Balbi said.
US Navy P-8 Poseidon patrol planes have joined an worldwide search for the Argentine Armada submarine San Juan, and the Navy has prepared submarine rescue vehicles and four uncrewed underwater vehicles (UUVs) to assist in the search as well.
The nature of the breakdown was not immediately clear.
This is the first time that an official has mentioned the sub encountering mechanical problems.
It said navy ships and aircraft were searching near the last known location of the vessel off the province of Chubut.
"It was therefore asked to change course and go to Mar del Plata", said Gabriel Galeazzi, the head of the naval base in the city, located 400 kilometers south of Buenos Aires.
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The ministry is analysing the sounds after seven distress signals reportedly heard on Saturday turned out to be bogus.
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.
Hope remains that the crew is alive and can be rescued.
"We don't know anything".
Macri was briefed on the search during his visit to the base. "We are waiting for you", read a message inscribed on a celestial blue-and-white Argentine flag hanging on the fence.
US satellite communications firm Iridium Communications, brought in to help with the analysis, said the signals did not originate from the submarine.
More than a dozen worldwide vessels and aircraft have joined the search, which has been hindered by stormy weather that has caused waves up to 20 feet (6 meters).
The Navy says the crew would have enough oxygen, food and water to last two weeks.
The US Southern Command on Sunday sent a second aircraft to assist in the operation, a P-8A Poseidon with a crew of 21 from Jacksonville, Florida, which is expected to arrive in Argentina in the coming hours. Angus Essenhigh, according to a statement from Britain's Royal Navy.
The submarine had been returning from a routine mission to Ushuaia, near the southernmost tip of South America, to Mar del Plata. Previously, the modern diesel-electric sub, built in 1983 and put into service in 1985, went through a mid-life overhaul, completed in 2013.