Father Maciel founded the order in 1941
Pope Benedict XVI has ordered a probe into the Legionaries of Christ, after the conservative order revealed its late founder had fathered a child.
The Vatican said a team of priests would carry out the investigation to help the Mexican order to deal with its problems with "truth and transparency".
In February, the order said its founder Marcial Maciel, who died in 2008, had fathered a daughter with a mistress.
The Vatican disciplined Father Maciel in 2006 over sexual abuse allegations.
Father Maciel was banned from exercising his ministry in public and told to retire to a life of prayer and penitence, following allegations that he sexually abused about 30 boys and young men over a period of 30 years.
The priest - who founded the conservative order in 1941 - had always denied any wrongdoing. He died in January 2008 at the age of 87.
The investigation into the Legionaries of Christ was announced in a letter by the Vatican Secretary of State, Cardinal Tarcisio Bertone.
The letter said the pontiff had decided to intervene "so that with truth and transparency, in a climate of fraternal and constructive dialogue, you will overcome the present difficulties".
The Vatican said that its investigators would visit all the institutions run by the Legionaries of Christ.
It was not until after Father Maciel's death that his secret life was revealed. In February, the order admitted that he had kept a mistress and fathered a daughter who was now in her 20s.
The disclosure caused consternation among the priests and laymen who are members of his religious congregation. They all take vows of poverty, chastity and obedience.
Father Maciel was close to the late Pope John Paul II.
The Legionaries of Christ order has about 600 priests and 2,500 seminarians, and says it has some 65,000 members around the world.