Media reports had suggested the trip would begin as soon as Sunday and last two days
The children from the Dalit community, India's lowest social caste, were on their way to their grandfather's house in the Shivpuri district in the central state of Madhya Pradesh on Wednesday.
"It was early morning and they had stopped to attend to nature's call" when they were attacked, police inspector general Raja Babu Singh said by phone.
"The kids were taken to the hospital but they succumbed to their injuries."
Two brothers had been arrested, one of whom appeared to be "mentally unsound", Singh added.
Modi is set to declare India free of open-air defecation on Wednesday, coinciding with the 150th birthday of independence hero Mahatma Gandhi, who also campaigned vigorously for better sanitation.
Modi, currently in his second term, launched his pet Clean India Mission in 2014, promising to build toilets for all by 2019.
His government says it has built more than 100 million toilets, particularly in rural areas, a major public health issue in the country of 1.3 billion people.
The multi-billion-dollar campaign combines raising awareness, subsidies for making latrines, and communal naming and shaming of those still relieving themselves in the open.
Critics, however, say lack of running water, poor maintenance and slow behaviour change are hampering the programme.
Catching those defecating in the open has previously resulted in violence.
In 2017, a man was lynched after he tried to stop authorities from photographing women who were defecating in the open.
A news channel earlier urged viewers to send in images of those defecating in the open so they could be shamed on national television.
The father of one of the children who died in the latest incident alleged his family had been facing discrimination from higher caste men.
"We don't have a toilet at home. The children went out to defecate in the morning," Manoj Balmiki was quoted as saying by the Press Trust of India news agency.
"The (brothers)... shouted at them for defecating on the road and rained sticks on their heads while the children were relieving themselves, killing them in seconds."
Media reports had suggested the trip would begin as soon as Sunday and last two days
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