Macri, 62, led the country from 2015 to 2019 and is now the leader of Argentina's rightwing opposition.
He is in the United States, but on his return home, will be barred from leaving again under an order issued Friday by judge Martin Bava.
Macri has been summoned for questioning on October 7.
The ARA San Juan sub disappeared in November 2017. When it was found just over a year later, it was at a depth of more than 900 meters in a desolate area of the South Atlantic some 400 kilometers off the coast of Argentina.
It had been crushed from an implosion apparently caused by a technical fault. Authorities decided against attempting to refloat it.
Family members of the 44 crew members told investigators they were followed and wiretapped, filmed and intimidated into abandoning any claims related to the incident.
Macri is accused of ordering the espionage. He risks between three and 10 years in jail for allegedly violating Argentina's intelligence laws.
Bava on Friday ordered the prosecution of secret service heads Gustavo Arribas and Silvia Majdalani, who reported to Macri at the time.
In March, two former Argentine military chiefs were sanctioned over the sinking.
Retired admiral Marcelo Srur was handed "45 days of arrest" for having given an "incomplete" picture to the defense ministry of what happened.
Claudio Villamide, the former commander of the Submarine Force, was dismissed after he was found guilty of a "lack of care and neglect of the troops and equipment under his charge."
Two active captains were given 20 and 30-day detentions and the former head of a naval base in the south of the country 15 days.
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