Regnum Christi, which is Latin for "Kingdom of Christ", released a statement on Friday announcing that Fr Oscar Turrion would leave the priesthood and included a chronology of events leading up to the revelation that the priest secretly fathered two children.
It read: "As those responsible for an institutions that is dedicated to the formation of candidates to the priesthood, we are conscious of the impact that the negative example of a formator and rector has on them and the Christian faithful.
"We are deeply saddened that the recent history of our congregation has quenched the fervor of some of our members. We are firmly committed to accompanying our brothers in moments of difficulty. Likewise, we reiterate our commitment to the path of renewal that we continue to follow led by the Church."
Fr Turrion, who was rector of the Pontifical International, wrote a letter in which he acknowledged the fact that he had children, apologised and requested prayers.
He said: "I never thought I would have to sit down to write words like these. At the same time I have always lived with the certainty that the truth ought to guide my life, cost what it may.
"Due to certain circumstances in the Congregation of the Legionaries of Christ and many other circumstances in the Church, I began to lose my grounding and became more and more disillusioned."
Revelations about the order's founder Rev Marcial Maciel Degollado, came to light between 2006 and 2014. The Vatican dismissed accusations by seminarians that Rev Degollado had sexually abused them - some when they were as young as 12.
Fr Turrion said he fell in love with a woman during this troubling time, which led to the birth of their son and a few months ago, their daughter.
The 49-year-old Spaniard told his superiors in March when his daughter was born. A new rector was appointed and Fr Turrion was ordered not to practice his ministry publicly.
Fr Turrion went on to say in his personal letter: "I want to add that I have not used any money from the exercise of my responsibilities as rector of the Pontifical College Maria Mater Ecclesiae. Rather I put aside donations that my friends gave me for my personal use; with this money I supported my children.
"I accept my responsibility. Without fear of the future, I put everything in God's hands and am resolved to continue "doing the truth" in my life.
"I am at peace and in harmony with God through the sacrament of confession."
