Fabiola Yanez, 43, and Fernandez, 65, who have a son, separated after he left office in 2023 and the scandal erupted when text messages detailing the alleged violence cropped up in a separate fraud investigation.
Yanez's lawyer, Juan Pablo Fioribello, told the La Nacion+ channel on Tuesday that messages detailing the alleged attacks, with photographic evidence, were found on the phone of Fernandez's private secretary, Maria Cantero.
The phone was being analyzed as part of a probe into influence peddling during Fernandez's administration.
After initially deciding not to press charges, Yanez later contacted the investigating judge "and told him, 'I want to file a criminal complaint. I want to denounce him (Fernandez) for the blows I received from him and the threats I have been suffering'," Fioribello said.
Argentine media reported that Fernandez has been forbidden from leaving the country amid the probe.
Fernandez has denied the accusation.
"The truth of the facts is different" and "it never happened," he said in a statement on the X social network.
He said that for "the integrity" of his children and "Fabiola herself" he would not make any statements and would only provide "evidence and testimony that will show what really happened."
The lawyer Fioribello, who has also represented Fernandez in other matters, said the former president denied hitting Yanez, but admitted the couple had bad arguments.