The February 22 quake caused severe damage to dozens of historic churches, most notably Christchurch Cathedral and the Catholic Cathedral of the Blessed Sacrament.
The majority of New Zealand churches - valued at several billion dollars - were insured by Ansvar Insurance New Zealand, which expected the Christchurch payout to be upwards of $200 million, Ansvar manager David Leather said.
Repairing Christchurch Cathedral, which was fully insured for an undisclosed sum, was likely to cost tens of millions of dollars.
Questions remained whether damaged structures would be rebuilt "like for like".
The full extent of the destruction would not be known until assessors were able to access the sites, and it appeared most of the damage was restricted to stone and masonry churches - wooden structures flexed more and survived better, he said.
"Our wish is to rebuild and restore these churches as to how they were before the earthquake happened, and our first approach is to achieve that goal."
As a result of the Christchurch earthquake, New Zealand churches faced higher insurance premiums, following the review of annual treaties with global reinsurers.
Otago-Southland Roman Catholic Diocese manager Stuart Young said the diocese had an estimated 40 churches - ranging from small, rural wooden churches to larger stone and brick structures - and not all were insured for full replacement because of the high premiums.
In the event of a major disaster, congregations would be faced with stark choices over future requirements, and there was no guarantee a significant church would be rebuilt, or even keep to the same site, he said.
In addition to rising premiums, building standards were likely to change, with churches faced with difficult decisions over the coming years.
"How are we going to strengthen these buildings? We don't have that sort of income," Mr Young said.
Margaret Fawcett, of the Presbyterian Church of Aotearoa New Zealand, said the church's insurance policies were for full replacement cover, and "we do expect an increase in premiums".
It was too early to speculate whether churches damaged in the quake would be rebuilt, she said.
Anglican Diocese of Dunedin manager Bronwyn Miller said the diocese, which owns 65 churches in Otago and Southland and dozens of other buildings, was warned premiums would rise following September's Canterbury earthquake.
The diocese now believed premiums would increase even more given the extent of the damage from last month's quake.
New valuations are being carried out on all Anglican churches, with Dunedin's St Paul's Cathedral valued at $23.2 million in 2008, up from $15.5 million in 2001.
If the cathedral was ever severely damaged, the diocese would enter discussions with "the parish, the city, the people of Dunedin and the Historic Places Trust" over its future.
"Rebuilding a cathedral does not take five minutes ... it takes years."
