The 49-year-old priest has served as an associate general secretary for the past five years. In his new post he succeeds Monsignor William Fay, who will leave the post in February after a five-year stint.
The general secretary serves a term of five years which can be extended for a year at a time.
Ordained in 1983, Father Malloy served as an associate pastor and later studied at the Pontifical Ecclesiastical Academy, in preparation for service in the papal diplomatic corps.
In the diplomatic corps, he served as secretary to the apostolic nunciatures in Pakistan and Syria. He also served as secretary to the Holy See’s mission to the United Nations in New York.
Meanwhile, the president of the bishops’ conference said Monday that priests maintain high morale and enjoy the appreciation of parishioners despite the clerical sex abuse scandals that have been reported in recent years.
In a speech defending the clergy, Bishop William Skylstad said that three recent studies show ”the high level of morale among priests” despite the abuse crisis and the pressures caused by a decline in vocations.