Union Minister of State for Rural Development Upendra Kushwaha also similarly faced public anger.
The toll from encephalitis has risen to 25 with 10 more children dying in Muzaffarpur in the last 12 hours, officials said.
People, mostly parents and relatives, protested when Manjhi, during a visit, enquired about the health of children admitted with suspected encephalitis to the government-run Sri Krishna Medical College and Hospital (SKMCH).
"We protested to express our resentment over negligence of health officials in providing proper treatment and lack of infrastructure," said Manish Kumar, a relative of a child.
Alarmed over the rising deaths from encephalitis, Manjhi along with Bihar's Health Minister Ramdhani Singh visited the SKMCH and instructed the doctors and district officials to provide all possible help to the children undergoing treatment.
"Manjhi also directed health and district officials concerned to take all precautionary measures to control the disease and ensure immediate treatment of affected children," Rajendra Prasad Ojha, a health official, said.
Kushwaha, who visited the hospital an hour before Manjhi, also faced public protest, with people demanding the central government's intervention in saving their children.
The people were pacified only after Kushwaha told them he will submit the report of his visit to Prime Minister Narendra Modi and urge him to send a high-level team of health experts to Muzaffarpur.
More than 30 children with suspected encephalitis have been admitted to various hospitals, a health official said.
Principal Secretary, health department, Deepak Kumar said an American team of experts, led by Jacob John, besides another one from Delhi is investigating the exact reason behind the deaths of children.
According to doctors, the acute encephalitis Syndrome is a severe case of encephalitis characterised by inflammation of the brain. Mosquitoes transmit the infection, resulting in high fever among the children.
"Every year, encephalitis hits Muzaffarpur, Gaya and other neighbouring districts in May or June. But this year, it seems to have struck a little late," a health department official said.
Early this year, the state government launched a special vaccination drive to cover thousands of children against encephalitis.
Last year, 62 children died of encephalitis in Muzaffarpur, and 150 died in 2012 in the district.
Most victims were from the poorest of the poor families and living in rural pockets of the state.