Syukur, 63, a Franciscan, announced his resignation before the diocesan curia council on Jan. 19, and the Vatican accepted it, according to sources in the diocese.
The Vatican has appointed Bishop Christophorus Tri Harsono of Purwokerto as the apostolic administrator until a new bishop is appointed.
The prelate said he resigned “not with a sense of loss but with freedom of heart,” and do not see it “as a human and worldly defeat.”
“I resigned not because I was guilty, but because I love the brotherhood and unity of the church, especially in the Diocese of Bogor," he said.
The resignation followed investigations by a Vatican-appointed team led by Holy Cross Bishop Antonius Subianto Bunjamin of Bandung, president of the Indonesian Bishops' Conference, to investigate several allegations against Syukur.
Bishop Bunjamin did not respond to UCA News' requests for comment on the case.
Last month, two diocesan priests — Bogor Diocesan Major Seminary rector, Father Yosep Sirilus Natet, and staff member Father Yoseph Kristinus Guntur — published an article accusing Syukur of authoritarianism, abuse of power, financial mismanagement, and of having personal relationships that influence all policies.
They cited the case of the bishop’s takeover of a hospital from the Franciscan Sisters of Sukabumi (SFS) and its transfer to lay management, which was described as an "expulsion" of the sisters and an abuse of power.
They also questioned Syukur's move to replace the diocesan curia officials in December, which they accused of being carried out secretly "without a spirit of synodality involving the old curia."
Though the decisions were later reversed following the Vatican engagement, these reportedly divided diocesan clergy, and Syukur became largely unpopular and sidelined.
Syukur, in a statement, defended his decisions as actions “out of love for the church and to avoid further confusion," and "as a form of my moral responsibility."
Regarding the hospital, he said that it was "a reorganization effort for the sake of a healthier mission," not an attempt to expel the sisters.
He also dismissed allegations of financial crisis and bankruptcy in the diocese and labelled the allegation of using diocesan funds for personal use as “baseness.”
The prelate also brushed off alleged inappropriate personal relationships with certain people, claiming they were “based on professionalism for the advancement of the diocese.”
On the conflict between priests and the curia, he said, "Leadership is often a lonely path."
He said in 2024, he was asked to decline cardinalship, “accused of allowing pedophilia to occur in the diocese."
He claimed he properly handled two cases of sexual abuse in his diocese and ensured the perpetrators ended up in jail.
A Church source told UCA News that, before resigning, Syukur had gone to the Vatican earlier this month to explain the accusations against him.
Born on the Catholic-majority island of Flores, Syukur has served as the Franciscan provincial of Indonesia twice since 2001.
He was appointed bishop of Bogor in 2013.
From 2021-2025, he served as the secretary general of the National Bishops’ Conference. Pope Francis named him a cardinal on Oct. 6, 2024, but he declined it.