The first hearing for Álvarez is scheduled for Jan. 10.
A warrant was also issued for a priest, the Rev. Uriel Vallejos, who had already reportedly left Nicaragua.
The move Tuesday was the latest chapter in a crackdown on the church by the administration of President Daniel Ortega, which expelled the nuns from Mother Teresa’s Sisters of Charity religious order.
In March, Nicaragua expelled the papal nuncio, the Vatican’s top diplomat in Nicaragua.
Bishop Alvarez has been under house arrest since August. He had been a key religious voice in discussions of Nicaragua’s future since 2018, when a wave of protests against Ortega’s government led to a sweeping crackdown on opponents.
Ortega’s government arrested dozens of opposition leaders last year, including seven potential presidential candidates. They were sentenced to prison this year in quick trials closed to the public.
Ortega has contended the pro-democracy protests were carried out with foreign backing and with the support of the Catholic church.
The former Marxist guerrilla infuriated the Vatican in the 1980s, but gradually forged an alliance with the church as he moved to regain the presidency in 2007 after a long period out of power.
But days before last year’s presidential election that resulted in Ortega winning a fourth consecutive term, he accused the Central American nation’s Catholic bishops of having drafted a political proposal in 2018 on behalf “of the terrorists, at the service of the Yankees.” He also contended the bishops were “also terrorists.”
In August, Pope Francis told thousands of people gathered in St. Peter’s Square that he was closely following with “worry and sorrow” events in Nicaragua that involve “persons and institutions.” He didn’t mention the detentions.
“I would like to express my conviction and my hope that through means of open and sincere dialogue, one can still find the bases for respectful and peaceful co-existence,″ the pope said.