In separate incidents in three other locations this week, 950 Indonesians had fallen ill as a result of food poisoning linked to the program, a member of a parliamentary commission overseeing health said.
President Prabowo Subianto launched the multibillion-dollar free meal program last year to improve nutrition for tens of millions of children but the costly scheme has been dogged by allegations of corruption, leadership changes and a spate of mass food poisoning outbreaks.
Improper food storage and late delivery of cooked meals are often to blame for the food poisoning.
In a senior high school in Lasem, Central Java, 752 students and 25 teachers have been suffering from diarrhoea and vomiting after consuming free meals on Wednesday, the school's principal Juhartutik said.
The students in Lasem were given grilled chicken.
Before it was distributed, a food taster found that some of it was "slimy", Juhartutik said.
"The slimy ones had already been set aside ... The kitchen operator said the food was cooked at 3am and it was eaten at noon," she said, adding that most of the victims were sent home.
Joko Paryanto, a local doctor who treated the victims, said 15 students and teachers have been hospitalised.
Sudaryono, head of the National Nutrition Agency which oversees the $US12.94 billion ($A17.96 billion) program, told parliamentary hearing that the food poisoning cases would be handled "seriously".
On Tuesday, 664 students fell ill in Sidoarjo, East Java, said Herawati Yuwantina, a local official.
The kitchen linked to the case was suspended on Wednesday.
In two other cases on Wednesday, 49 people in the East Java city of Nganjuk and 237 in the West Sumatra region of Agam contracted food poisoning, said Charles Honoris, an MP and member of the sole political party outside the governing coalition, citing health department data.
Charles wrote on Instagram that they were not isolated incidents.
"This is a failure of the system," he said.
As of Tuesday, 50,000 individuals had been affected by food poisoning cases, Charles said, citing health department data.
In July, a survey by pollster Saiful Mujani Research and Consulting showed only one-third of people were satisfied with the scheme, with poisoning cases cited as a major reason.
