Argentina's navy said a "noise" picked up by sonar on Monday during the search did not come from the vessel.
The ARA San Juan submarine, with 44 crewmen on board, last communicated with their command base on November 15.
Gabriel Galeazzi, a naval commander, told reporters that the submarine had come up from the depths and reported an electrical malfunction before it disappeared 268 miles (432 km) off the coast.
Hopes that it had been found were kindled earlier after two Argentinian navy vessels detected "a continuing noise" on the route where it disappeared.
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"The submarine surfaced and reported a malfunction, which is why its ground command ordered it to return to its naval base at Mar del Plata", he said.
Navy spokesman Enrique Balbi said the low-frequency satellite signals received Saturday lasted a "few seconds", but had not connected with a base, partly due to inclement weather.
However, Argentina's navy will take advantage of better weather conditions Tuesday and continue searching for the submarine. The US provided several planes too and unmanned underwater vehicle to help in the search and rescue operation.
This type of problem is considered routine, and the crew was reported safe, he added.
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Under normal circumstances, the vessel has sufficient fuel, water, oil and oxygen to operate for weeks without external help, Balbi said, and the vessel could "snorkel" - or raise a tube to the surface - "to charge batteries and draw fresh air for the crew".
There was one more communication with the captain before the sub went missing, Galeazzi said.
The German-built San Juan submarine has been missing since Wednesday when it reported a battery failure and lost contact with the Argentine Navy. "This is why we are deploying all resources with high tech sensors". Courtesy Ronald Gutridge/U.S. Navy/Handout via REUTERS ATTENTION EDITORS - THIS IMAGE HAS BEEN SUPPLIED BY A THIRD PARTY."Today is a critical day", said Maria Victoria Morales, the mother of Luis Garcia, an electrical technician aboard the vessel.
US satellite communications company Iridium Communications Inc, which was brought in to help analyze the calls, said they did not originate with its device aboard the vessel and may have been from another satellite communications company's equipment.
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More than a dozen worldwide vessels and aircraft have joined the search for the missing submarine, which has been set back by stormy weather that has caused waves up to 20 feet.