Four people were believed to have been inside Loon's Our Lady of Light church when it collapsed, according to Balakayo, the priest.
He said they remained unaccounted for, but locals had given up hope they were still alive.
In front of the rubble of the church an improvised altar had been erected with a lone statue of the Virgin Mary, where teary residents stopped by to make the sign of the cross.
Ten churches, many of them dating back centuries to Spanish colonial rule of the Philippines, were destroyed or badly damaged on Bohol and the neighbouring island of Cebu.
Video footage broadcast by AFP on Wednesday showed an elderly woman narrowly avoiding being crushed by the collapsing bell tower of the Philippines' oldest church, Cebu's Basilica Minore de Santo Nino (Basilica of the Child Jesus).
Most of the deaths were on Bohol, which is one of the most popular tourist islands in the Philippines because of its beautiful beaches, rolling "Chocolate Hills" and tiny "tarsier" primates.
The number of confirmed fatalities on Bohol jumped to 141 as authorities in isolated towns restored communications and reported dozens more deaths, the head of the province's information office, Augustus Escobia, told AFP.
Nine people died on Cebu province, home to the Philippines' second-biggest city of the same name, while another person was confirmed killed on nearby Siquijor island.
Survivors were further tormented on Wednesday by incessant aftershocks, including some exceeding 5.1, according to national disaster authorities.
President Benigno Aquino visited Bohol and Cebu to oversee rescue efforts, and sought to reassure survivors as the number of aftershocks surpassed 800.
"The bottom line is we do not have to fear that something stronger than... (Tuesday's quake) is coming," Aquino said in a nationally televised meeting with cabinet members at Tagbilaran, Bohol's capital.
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