Vatican spokesman Alessandro Gisotti stressed that the allegations against Bishop Gustavo Zanchetta only emerged in recent months, nearly a year after Pope Francis created the new position for him as "assessor" of the Holy See's office of financial administration.
At the time of his July 2017 resignation, Zanchetta had only asked Francis to let him leave the northern Argentine diocese of Oran because he had difficult relations with its priests and was "unable to govern the clergy", Mr Gisotti said.
Pending the preliminary investigation into allegations of sexual abuse under way in Argentina, 54-year-old Zanchetta will abstain from work at the Vatican, he said.
The case could become yet another problem for Francis, who is already battling to gain trust from the Catholic flock over his handling of sex abuse and sexual misconduct, stemming in particular from the scandal of ex-cardinal Theodore McCarrick.
Francis's standing would take another hit if he personally intervened to help out a bishop from his native Argentina - finding a job for him during limited Vatican hiring - and the man later turned out to have credible allegations of misconduct against him.
Zanchetta's hasty departure from Oran on July 29 2017 was mired in mystery. He did not celebrate a farewell Mass, as might be expected, and he issued a cryptic statement saying he had been suffering a "health problem" for some time, had just returned from the Vatican where he presented his resignation to Francis, and needed to leave immediately for treatment.
A statement issued the same day from his vicar general said Zanchetta had already left Oran, a conservative and poor diocese near Argentina's northern border with Bolivia that Zanchetta had run since Francis made him a bishop in 2013 in one of his first Argentine episcopal appointments.
Zanchetta, the vicar said at the time, would be staying in Corrientes - several hundred miles away - as a guest of the archbishop until Francis accepted his resignation.
Often such procedures can take months, but the Vatican announced Francis had accepted it three days later, on August 1.
Zanchetta then disappeared from view until December 19 2017, when the Vatican announced he had been named assessor of APSA, the office that manages the Vatican's vast real estate and other financial holdings.
The appointment immediately raised eyebrows, but Zanchetta appeared to have settled in well at APSA, and Mr Gisotti said Francis appointed him because he had an established capacity for administrative management.
It was not immediately clear what Zanchetta's health problems were at the time of his resignation, but by all indications there were grave problems with his leadership and divisions within the diocesan clergy.
"The reason for his resignation is linked to his difficulty in handling relations with the diocesan clergy, some of which were very tense," Mr Gisotti said.
"At the time of his resignation there were accusations against him of authoritarianism, but there were no accusations of sexual abuse against him."
The allegations were levelled internally in recent months, Mr Gisotti said, and last week the provincial newspaper in Salta, El Tribuno, reported that three priests had brought accusations against him to the Vatican's ambassador in Buenos Aires.
The newspaper said the priests had lodged accusations of abuse of power, economic abuse and sexual abuse inside the seminary.
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