The comments by Cardinal William Levada, a high-ranking Vatican official until recently, came in the wake of a grass-roots campaign to shame Mahony into refraining from participating because of his role protecting sexually abusive priests.
Mahony left for Rome over the weekend after recently released church documents showed he had covered up for other priests who raped and molested children.
"There are some victims groups for whom enough is never enough, so we have to do our jobs as best we see it," said Levada, 76, who spoke with reporters from a Menlo Park seminary as he prepared for his trip to the Vatican for the papal conclave.
"He has apologized for errors in judgment that were made," Levada said. "I believe he should be at the conclave."
On Monday, Mahony took to social media and his own personal blog to write about persecution and forgiving one's enemies. He said he has a special prayer group for people who "cannot forgive me for my past hurts and offenses," including members of the media, attorneys, protesters and those who "hate and despise me."
He also tweeted from Rome, writing: "Anyone interested in loving your enemies, or doing good to those who persecute you? See my blog for today. Wow, Jesus is demanding."
Levada said Cardinal Keith O'Brien's decision Monday to step down as archbishop of St. Andrews and Edinburgh and to opt out of the conclave will "provide the freedom to do a good independent investigation and decide on appropriate measures to take on this case."
Levada, who leaves for Rome on Tuesday, retired in 2012 after spending six years as the head of the Congregation for the Doctrine of the Faith, the Vatican's orthodoxy watchdog, which also defrocked pedophile priests.
He played a key role in several church sex-abuse reforms. While serving previously as an archbishop in California and Oregon, he kept some accused molesters in the church and failed to share some allegations with police or parishioners.
On Monday, Levada drew a sharp divide between gay men and pedophile priests.
"By nature homosexuality is a not a predatory activity, it is a sexual activity that the Catholic church does not condone," he said. By contrast, he said pedophile priests are violating the sanctity and purity of young people.
Levada also said bureaucratic reforms at the Vatican will require a lot of attention from the next pope. He said he'll be looking for a candidate with deep faith, someone who has shown leadership and has language skills. He said youth is also a factor, and he extinguished any rumors that the next pope might be from the U.S.
"I don't know what the Las Vegas oddsmakers are saying today," he said, "but I don't think it's likely that we would see an American pope. It would be an additional complexity for an American pope to have to deal with the perception that some of his decisions might be perceived to be dictated by American governmental policy."
Levada also said he respects Pope Benedict's decision to withhold findings from an investigation into Vatican leaks to cardinals voting on his successor.
"If his judgment is that there's nothing in that report that's necessary for the cardinals then I think we can rely on that," he said. "Pope Benedict is a man of very good judgment."
Levada and Mahony will join more than 100 cardinals on Thursday in Rome to begin the historical process that will choose a successor to Pope Benedict XVI, whose decision to retire took worldwide Catholics by surprise.
Levada, whose Vatican job was held by the former Cardinal Joseph Ratzinger before he became Pope Benedict XVI, said in all his years of service, he never anticipated being called to a conclave.
"Never. Never," he said. "It's very challenging. It's pretty exciting."
Prior to the election, the cardinals meet and discuss the qualities of the candidates.
"We begin to make some judgments," he said.
Then, in silence, the cardinals vote, sometimes repeatedly, tucking ballots into a closely observed box which is then openly counted in front of them.