The students from the San Jose Elementary School in the town of Mabini had eaten snacks made from cassava roots in their mid-morning break before falling ill, officials said on Wednesday.
Philip Fuderanan, a spokesman for the mayor of Mabini, said 25 of 60 children who had fallen ill and been taken to various nearby hospitals had died.
"As of 4pm, the number of casualties has reached 25," Fuderanan told local GMA television.
Eutiqio Bernales, mayor of the neighbouring town of Ubay where most of the children were taken for treatment, said medical workers were numbering those dead at 28.
"In fact, I borrowed a dump truck to take back (to Mabini) the more than 20 bodies here," Bernales said, adding that shocked and grieving relatives of those who died were being properly looked after.
Fuderanan said municipal health workers had rushed to the hospitals to carry out tests on the surviving children, many of whom were in critical condition.
"They had eaten food with cassava as an ingredient," Fuderanan said after the initial results of an investigation by doctors.
Municipal health authorities were investigating the incident, and radio reports said two vendors who had sold the children the snack were being questioned.
"As of 4pm, the
number of casualties
has reached 25"
spokesman for Mabini mayor
"We are trying to account for all the children who had eaten (the root crop). We are checking them up to make sure that they are all right," vice mayor of Mabini Ester Tabigi said.
"Twenty-five did not make it and expired," she said.
Cassava or manioc is a tropical food crop widely grown around the Asian region. In many impoverished Philippine towns, it is a substitute to rice, the staple food.
Cassava is traditionally boiled, or processed as ingredients for native cakes and delicacies in the Philippines.
Experts say that certain types of cassava may contain substances that produce cyanide and are toxic to humans if unprocessed.
Doctor Nenita Po, who heads the state hospital in Bohol's capital city Tagbilaran, about 100km east of Mabini, said doctors there took in 13 patients. Two of those later died.
A 68-year-old woman who reportedly prepared the food that the children ate was among those still sick in the Tagbilaran hospital, Po said.
"When they arrived here they were vomiting, complaining of abdominal pains and LBM (Loose Bowel Movement or Diarrhoea)," she said.