Canon Patrick McEntee requested a leave of absence last year while a serious safeguarding investigation was carried out.
The 69-year-old, from Esker Road, Dromore, is charged with four counts of indecently assaulting one complainant on dates between 1988 and 1989.
There is also a single count of indecently assaulting another complainant between 1980 and 1981.
No details surrounding the circumstances of the alleged offences were disclosed during the short hearing, although it is understood they relate to McEntee’s time in Co Fermanagh.
McEntee appeared in the dock of Dungannon Crown Court, pleading not guilty to each charge in turn.
Defence counsel said a number of pieces of additional evidence are to be sought, which should be available in the coming months.Judge Fiona Bagnall remanded McEntee on continuing bail of £500 and ordered him to return for trial on September 23, which is expected to last around one week.
As part of bail conditions, McEntee is to reside at his current address, and no other, and is also banned from all contact with the complainants and any person aged under 16.
Originally from Monaghan, McEntee joined the staff of St Michael’s College, Enniskillen, in 1977, teaching religious studies and sitting on the Board of Governors.
He was also college president between 1994 and 2000, moving on to take up the post of Parish Priest at St Davog’s church in Dromore, in 2001, where he has remained until his recent leave of absence.
Previously, the Diocese of Clogher confirmed: “Canon Patrick McEntee PP, Dromore, Co Tyrone, has asked for a period of leave to allow a safeguarding matter to be addressed.
"The Diocese of Clogher has robust safeguarding policies and practices in place. The Diocese of Clogher takes seriously all allegations, suspicions or concerns of abuse.”
Asked about McEntee’s current status given the charges he faces, a spokesperson replied: “Canon Patrick McEntee is on leave while a safeguarding matter is dealt with and will continue to be on leave from ministry until all due processes have been completed.”