Meredith Catholic priest John Haines has quit his post after police charged him over a series of alleged indecent acts with children.
Police raided Fr Haines' home last Friday, seizing images of children before taking him in for questioning at Colac police station.
The 61-year-old was later charged with possession of child pornography, transmitting child pornography, procuring a child for child pornography and attempting to procure a child for child pornography.
He was also charged with two counts of indecent assault with a child under 16 and one count of indecent assault.
Melbourne's Catholic Archbishop Denis Hart confirmed he had accepted the resignation of Fr Haines, who he named in a prepared statement.
Fr Haines has been placed on administrative leave and his faculties to operate as a priest withdrawn, the Catholic Archdiocese of Melbourne said.
"I am deeply troubled by the laying of charges and concerned for all persons involved,'' Archbishop Hart said.
"I wish to assure parishioners and the local community of my support and concern for them at this time.''
Archbishop Hart said Fr Haines was entitled to the presumption of innocence.
"As the matter is now in the hands of the Victoria Police it is not appropriate for me to make any further comment,'' Archbishop Hart said.
Det-Sgt Bill Caldow, of Colac CIU, said the alleged offences occurred last year and early this year.
"They've allegedly occurred in 2007 and 2008 in the Geelong district,'' he said.
"We executed the search warrant after acting on a complaint made to Colac police.''
Fr Haines led the St Joseph's Catholic parish, which takes in Meredith, Winchelsea, Anakie, Bannockburn, Elaine, Inverleigh and Lethbridge, for 12 years.
He tendered his resignation to the Melbourne archdiocese following his charges and has been given administrative leave.
Parish council chairwoman Diane Ritchie said the church's local assembly was devastated by the allegations and by Fr Haines' departure.
"We're completely devastated by what has happened but he was a wonderful country pastor,'' Mrs Ritchie said.
"We're just trying to keep the place going. It's a really close and vibrant parish and we'll support each other.''
Melbourne archdiocese vicar-general Monsignor Les Tomlinson said arrangements had been made to cover the parish's services following Fr Haines' resignation.
"Obviously we'll have to give it some thought as to how we provide for the parish in the future. We haven't reached any proposal but at this stage we'll arrange for replacements for weekends until something more permanent can be organised,'' Monsignor Tomlinson said.
"I have visited the parish on a number of occasions and I've always found it a delight to visit, so I'm certainly keen for us to provide for the parish in such a way that it will continue to grow.''
Monsignor Tomlinson declined to comment on the circumstances surrounding Fr Haines' resignation, but thanked nearby parishes for their help following the popular priest's departure.
"The fact that he has chosen to resign was his decision. We acknowledge that charges have been brought against Fr Haines but we will wait for the process of the law to take its course,'' he said.
Fr Haines will appear at Geelong Magistrates' Court on May 29.
