The new service is provided by the charity Living Room Cardiff and will offer support on everything from money worries to addictions.
It will take over from the current Church Counselling Service which was set up 20 years ago.
The 'Cynnal' service is a free confidential counselling service available throughout Wales for all members of the Clergy and their families who might be facing challenging times in their personal lives.
Wynford Ellis Owen, chief executive of Living Room Cardiff said: "Clergy are perceived as people who don't have problems - they are the ones we go to when we have problems.
"But they are human like the rest of us and sometimes, under pressure, their problems - and those they are helping others with - can come to the fore.
"That can be particularly difficult for them because they work across the community.
"We can provide them and their families with a safe environment where they can seek help and support in confidence."
The Archbishop of Wales, Dr Barry Morgan said: "The Church in Wales welcomes this new service for the care and welfare of our clergy and is keen to support it."
Premier's Antony Bushfield speaking to Wynford Ellis Owen: