Of all the opposition to the Jesuits that led to the suppression perhaps the most damaging was from within the Church. A precursor to this intra-church rivalry was the 'De Auxilis' controversy in the sixteenth century between the Jesuits and the Dominicans. In someways the damaging Jansenist dispute with the echoes this controversy. The nub of the crisis was the question of how God's grace operated with human free-will - specifically what help it provided hence 'De Auxilis' . The Dominicans declared that the Jesuits conceded too much to free will, and so tended toward Pelagianism. In turn, the Jesuits complained that the Dominicans did not sufficiently safeguard human liberty, and seemed in consequence to lean towards Calvinism.
The controversy is usually supposed to have begun in the year 1581 Prudencio de Montemayor SJ defended certain theses on grace which were vigorously attacked by the Dominican Domingo Baûez. The controversy went on for years, passing through three phases — in Louvain, in Spain, and in Rome. At Louvain was the famous Michel Baius, whose propositions were condemned by the Church. The Jesuit (afterwards Cardinal) Francisco de Toledo, authorized by Gregory XIII, had obliged Baius, in 1580, to retract his errors in presence of the entire university. Baius thereupon conceived a deep aversion for the Jesuits and determined to have revenge
A commission established by Pope Clement VIII to settle the theological controversy . Between 1594 and 1597 twelve reports were submitted; by the three universities of Salamanca, Alcalç, and Sigüenza; by six bishops , Miguel Salon (Augustinian Friar), Castro (Canon of Toledo), and Luis Coloma, Prior of the Augustinians at Valladolid. There upon Clement VIII ordered the generals of the Dominicans and the Jesuits, respectively, to appear with some of their theologians before the commission, explain their doctrines, and settle their differences. In obedience to this command both general began today (22 February, 1599) before the commission a series of conferences which lasted through that year. Bellarmine, created cardinal in March, was admitted to the sessions. . Sixty-eight sessions were thus held (1602-1605).
Clement VIII died 5 March, 1605, and after the brief reign of Leo IX, Paul V ascended the papal throne. In his presence seventeen debates took place. Finally, after twenty years of discussion public and private, and eighty-five conferences in the presence of the popes, the question was not solved but an end was put to the disputes. The pope's decree communicated (5 September, 1607) to both Dominicans and Jesuits, allowed each party to defend its own doctrine, enjoined each from censoring or condemning the opposite opinion, and commanded them to await, as loyal sons of the Church, the final decision of the Apostolic See. That decision, however, has not been reached.