Danny Foley, 35, of Listowel, was convicted on Wednesday of sexually assaulting a 22-year-old woman.
Before sentencing, Father Sean Sheehy queued, along with other local people, to shake hands with Foley.
Bishop of Kerry William Murphy said he wished to dissociate himself and the diocese from the priest's actions.
"I wish to offer my sympathy to the victim and apologise to her on my own behalf and on behalf of the diocese of Kerry," he said.
"I pay tribute to her courage. I hope what has happened will not undermine the progress that has been made in bringing perpetrators of sexual abuse to justice."
'Harsh'
Fr Sheehy, who has known Danny Foley since he was a teenager, also provided him with a character reference in which he said he was always respectful to women.
He said he shook his hand with the best of intentions and would do so again.
Fr Sheehy later told the Newstalk radio station that he believed Foley's seven year jail sentence was "extremely harsh".
He added that he had no regrets about supplying the character reference.
The victim of the assault was found in a semi-conscious state, naked from the waist down, with extensive bruising and scratching on 15 June 2008.
Foley had initially told police he found her lying next to a skip but changed his story after CCTV footage showed him carrying her to the area.
A jury gave a unanimous guilty verdict.
The trail judge said Foley had used "odious" language to describe his victim and his allegations about mutual sexual acts on the night, were designed "to add insult to injury" and to "demean and denigrate" her.
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SIC: BBC