The order last month announced it would not cooperate with a Church investigation
The head of the Knights of Malta has announced his resignation amid a bitter row with the Vatican.
The dispute between Pope Francis and the order's Grand Master Matthew Festing broke out following the ousting of the order's Grand Chancellor Albrecht von Boeselager last month.
He was sacked after allegations that the order's charitable wing had distributed condoms during a medical project in Myanmar. The use of artificial contraception is banned by the Catholic Church, which the order has been historically linked with.
The sacking came despite von Boeselager - who was serving as the order's health minister at the time of the programme - saying he stopped the condom programme as soon as he learned of its existence.
He refused to resign over the matter, with the Knights of Malta saying such a refusal to obey the command of a Grand Master, no matter the reason, "is disgraceful".
According to The Guardian, von Boeselager and supporters claimed the controversy over the condom issue was an excuse for Festing and conservative members of the Church to increase their power - amid moves by the more liberal Pope Francis to 'reform' the Church, including over the contraceptive issue.
Last month, the Vatican announced it had launched an investigation into the sacking.
The Knights of Malta publicly announced it would not cooperate with the investigation in order to "protect its sovereignty" - a move seen as a significant escalation of the row.
The resignation of the Grand Master of the organisation - which was founded in the 11th century, and has more than 13,000 members - is unusual, as leaders of the order usually hold the position for life.
He agreed to resign following a meeting with Pope Francis.
In a statement, the Knights of Malta said: "The Grand Magistry of the Sovereign Order of Malta announces that Grand Master Fra’ Matthew Festing has convened an extraordinary session of the Sovereign Council for 28 January 2017 for the acceptance of his resignation from the office of Grand Master".
The Vatican confirmed that the Pope had accepted the resignation, and that a papal delegate would be appointed to oversee the organisation until a new leader is elected.
"[Pope Francis expressed] appreciation and gratitude to Fra’ Festing for his loyalty and devotion to the Successor of Peter, and his willingness to serve humbly the good of the Order and the Church," the Church said in a statement.
"The governance of the Order will be undertaken ad interim by the Grand Commander pending the appointment of the Papal Delegate."