The devout Roman Catholic said after giving it "serious thought" he could not agree with the church's stand on the issue.
Scalia questioned the church's opposition to the death penalty late last month at a conference on the subject in Chicago. He was asked about it again Monday at Georgetown University, a Catholic school.
The Vatican under Pope John Paul II has been strongly anti-death penalty, and the pope has personally appealed to leaders to commute death sentences. In 1999, he said capital punishment, abortion, euthanasia and assisted suicide are part of a "culture of death."
Scalia told Georgetown students that the church has a much longer history of endorsing capital punishment.
"No authority that I know of denies the 2,000-year-old tradition of the church approving capital punishment," he said. "I don't see why there's been a change."
Scalia, a father of nine, including one priest, attended Georgetown as an undergraduate and later taught there as a visiting professor. He talked about the cultural move away from faith before answering questions from students.
In Chicago on Jan. 25, Scalia said, "In my view, the choice for the judge who believes the death penalty to be immoral is resignation rather than simply ignoring duly enacted constitutional laws and sabotaging the death penalty." His remarks were transcribed by the event sponsor, the Pew Forum.
Scalia said Monday that "any Catholic jurist (with such concerns) ... would have to resign."
"You couldn't function as a judge," he said.
Some in the crowd applauded when a female student asked Scalia to reconcile his religious beliefs with his capital punishment votes on the court. Scalia, 65, is one of the court's most conservative members and has consistently upheld capital cases.
Freshman Sean Kiernan said later that he was disappointed that Scalia talked about the importance of his religion, then took a stand contradicting the church. "I don't think it's correct," he said.
"He's got a lot of courage and conviction," said Stephen Feiler, the student who organized the event to celebrate Jesuit heritage.
By Gina Holland © MMII The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed