Church spokesman Francis Sullivan says they are ready for whatever comes out of the investigation.
"All the truth must come out, and some of that truth will be painful and some of it will require us admitting that in the past there were cover-ups," he said.
The letter calls on the church's faithful to join in special days of penance in the wake of the abuse crisis and urges them to say extra prayers.
Mr Sullivan says the letter is about starting the process of atonement.
"We are seeking reconciliation, we are seeking to embrace the truth of what's happened so that a just outcome and a process of healing can occur," he said.
'This is a pastoral letter which is very much at the heart of that exercise."