The comments from Rev Adrian Dorrian come the day after Sinn Fein said that it would not elect a new deputy first minister by Monday's 4.00pm deadline.
Speaking on Premier News Hour, the chair of the Church of Ireland's Church and Society Commission said the situation is disappointing.
"We've had crises before and we've managed to work our way through them but it's very frustrating when you think there's so much you'd like to see happening in terms of our regional government and yet the parties seem unable to come to a consensus to allow that government to get into operation again."
Northern Ireland Secretary, James Brokenshire, must now decide whether to call a fresh election, allow Westminster to take control or continue to try to work toward finding a compromise between Sinn Fein and the DUP.
Rev Dorrian told the News Hour that cooperation was the best way forward.
"I think there would be a lot of dissatisfaction with another election," he said. "Although I think it's a very real possibility. Likewise, direct rule is a hot potato and while it may begin to get things done it's not a long term solution."
He added that it was important for Christians to pray for leaders at this time.
"I think to pray for wisdom for the British and Irish governments and the role that they might play in these on-going conversations and of course the politicians in Northern Ireland. All parties are blaming each other and while there may be truth in that, grace is a very important focus for prayer."
Listen to Marcus Jones speak to Rev Adrian Dorrian here: