The former Guards officer Matthew Festing resigned from his post on January 25 after clashing with the Holy See over his dismissal of a senior deputy in December.
The row focused on the distribution of condoms as part of an aid project run by the ancient order in southeast Asia and highlighted deep divisions within the organisation that was founded in 1113.
Mr Festing’s deputy Albrecht von Boeselager was later reinstated in a move that was seen by some as a humiliation for the then Grand Master, triggering his resignation.
Matthew Festing (L) with Pope Francis in 2014
An election for his replacement will now take place in Rome on April 29.
However, Pope Francis’ delegate to the Knights, Archbishop Angelo Becciu has now written to Mr Festing and told him in unequivocal terms to stay away.
The Archbishop wrote on April 15: “With a view to the complete Council of State (the election), many have expressed their wish that you not come to Rome and participate in the voting sessions.
Members of the Knights of Malta (archive image)
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“Your presence would reopen wounds, only recently healed, and would prevent the event taking place in an atmosphere of peace and regained harmony.”
Pope Francis had endorsed the request that Mr Festing not come to Rome, Archbishop Becciu wrote.
He asked Mr Festing, who remains a member of the order, to abide by the request “as an act of obedience” to the Holy Father.
Matthew Festing (L) with Pope Francis in June last year
Mr Festing had previously indicated in an interview with the Catholic Herald that he would go to Rome for the election.
A Knights of Malta insider told The Telegraph: “Given the tone of the letter, it would seem appropriate to abide by it.”
The Sovereign Military Hospitaller Order of Saint John of Jerusalem of Rhodes and of Malta, to give it its full name, is the world’s oldest surviving chivalric order and started life a the Knights Hospitaller in Jerusalem in about 1099.
The order has a total of 13,500 knights, dames and auxiliary members as well as around 80,000 volunteers that work in over 120 countries doing charity work.