Ms Main asked her councillors to consider a "practical and reasonable" resolution to the matter, such as moving the prayer to the beginning of the council meeting.
"This issue has preoccupied both the public and the media, with a consequent perception that this council is wasting both time and money on an issue which could be solved in a way which avoids further disharmony," the mayor said.
Councillor Michael Laws said he was bemused the prayer was being discussed again. He said the compromise suggested by Ms Main would in effect remove the prayer altogether.
"The council should be more overt about it," Mr Laws said.
He said he did not see how the compromise solved the problem.
"It doesn't deal with Mr Solomon's concerns," Mr Laws said.
In reply, Mr Solomon said he was willing to accept moving the prayer to the start of the meeting "in the spirit of compromise".
Councillor Allan Anderson, who co-wrote the prayer, spoke passionately that the prayer should remain as part of the meeting. He cited the significant contribution churches and Christian organisations made to the well-being of the Wanganui community.
"Is it asking too much from council to honour that contribution in the manner we always have?" Mr Anderson said.
He said Mr Solomon's threats of legal action if the prayer remained as part of the agenda amounted to blackmail.
"Currently we have one councillor threatening mayhem and financial penalty if we don't accede to his demands.
"However, at least council now has the dubious honour of joining some 50 other Wanganui citizens who have been either served or threatened with litigation by this one councillor who has an abysmal record of attendance and contribution to this body."
Councillor Hamish McDouall was one of three councillors to abstain from voting and his mixed feelings on the prayer issue were evident in his unusually hesitant manner of speaking.
"Five members of this council are also on the Whanganui District Health Board. The board starts its meeting sometimes with silent reflection, sometimes with a Christian prayer, sometimes with some wise words being shared. I think that is a good compromise. I would have been happy with that."
Mr McDouall criticised Mr Anderson for his attack on Mr Solomon: "I would suggest that Councillor Anderson's clarity of mind has been somewhat distorted by personal enmity."
Ms Main described the decisions as pragmatic and providing a reasonable compromise.
"It will allow those who wish to participate in a prayer or reflection to do so immediately before our council meetings start. Those with an alternative view will also be provided for by removing the prayer from the meeting agenda.
"This issue has caused considerable disharmony within the Council and in the community. The compromise we have reached recognises the diversity of views in our community and will allow us all to move forward."