Monsignor Angelo Becciu will work in "close collaboration" with the order's interim leadership, after Grand Master Matthew Festing was forced to relinquish his post last month.
Becciu's mandate to oversee "a spiritual and moral renewal of the order" will expire once a new grand master has been elected, after a council meeting expected to be held within three months.
In the meantime, Becciu will be Francis' "sole spokesman" with regards to the order, suggesting that prominent US conservative Cardinal Raymond Burke will no longer act as the pope's liaison to the group.
Burke has been outspoken in his disapproval of Francis' efforts to reform Church teaching on questions related to the family, marriage and divorce.
The dispute between the knights and the Vatican erupted into public view in December, when the order's grand chancellor, Albrecht Boeselager, was dismissed.
Press reports claimed that Boeselager oversaw charities that took part in a programme offering free condoms to prostitutes and others in Myanmar, but his dismissal had been seen by some as the result of his being too liberal for Burke.
After weeks of tension, Francis secured Boeselager's reinstatement.
"The accusations against me are without merit, and my conscience is clean", Boeselager said at a press conference last Thursday, adding that he had stopped the condom distributions as soon as he learned of them.
He attributed the dispute to "growing tensions" between elected members of the order and advisers with no official role who had "poorly advised" the former grand master.
The Order of Malta was founded in Jerusalem in 1048 as a community of hospitals caring for the sick. It now operates in 120 countries, managing hospitals and clinics, with 13,500 members and 100,000 employees and volunteers.