Leaders of the Catholic diocese of St. Poelten, about 50 miles west of Vienna where the seminary is located, spent much of Monday in an emergency meeting.
Politicians and church leaders called for the removal of Bishop Kurt Krenn, who oversees the diocese. Krenn, a conservative churchman, angered many in overwhelmingly Catholic Austria by dismissing the images as a "childish prank" and refusing to resign.
The seminary's director, the Rev. Ulrich Kuechl, resigned along with his deputy, Wolfgang Rothe, the diocese said after the meeting. It did not elaborate.
Up to 40,000 photos and an undisclosed number of films, including child pornography, were found a year ago on computers at the seminary, the respected news magazine Profil reported.
It published several images purportedly showing young priests and their instructors kissing and fondling each other, and said others showed them engaging in orgies and sex games. The child porn came mostly from Web sites based in Poland, the magazine said.
Hannes Jarolim, a spokesman for the opposition Socialist Party, urged the Interior Ministry on Monday to launch a criminal investigation. Public prosecutor Walter Nemec said local police were examining the material, which he said showed seminarians "in perverse situations together with their superiors."
The Austrian Bishops Conference, meanwhile, issued a statement pledging a full and swift internal investigation.
"Anything that has to do with the practice of homosexuality or pornography has no place at a seminary for priests," it said.
Krenn, the embattled bishop, told Austrian television he had seen photos of seminary leaders in sexual situations with students, but he described the images as part of an elaborate prank that "had nothing to do with homosexuality."
His nonchalance drew swift and scathing reaction from across Austria.
"Collecting child pornography cannot be dismissed as a prank," said Thomas Huber, a Green Party politician.
In the mid-1990s, Austria was stung by allegations that Cardinal Hans Hermann Groer, who died last year, had molested students at an all-male Catholic boarding school two decades earlier. The affair had prompted Groer to step down.
A group of St. Poelten Diocese officials planned to ask the Vatican to remove Krenn as bishop, Austrian radio reported Monday. Martin Walchhofer, who supervises the alpine country's seminaries, said Krenn ultimately was responsible and "must answer before the church and before God for all of this."
Asked whether he intended to resign, Krenn said bluntly: "No."
The Vatican said it had no comment.
Krenn, 68, issued a statement calling the accusations groundless while conceding that he "may have made some wrong personnel decisions" at the seminary. Rothe, the former deputy seminary chief, was a legal adviser to the bishop.