The issue sparked off a furore in the state.
The incident occurred on June 10 (Sunday), but came to the fore only after some videos of the boys' parading in the Vakadi village went viral even as the authorities swung into action.
The incident came as a major embarrassment for the ruling Bharatiya Janata Party-Shiv Sena combine even as Chief Minister Devendra Fadnavis is on a tour of Dubai, Canada and US to attract investments.
State Social Justice Minister Dilip Kamble told media persons that two persons have been arrested in this connection and further investigations are underway.Read | 3 children die after boiling water falls on them
Union Social Welfare Minister Ramdas Athawale condemned the incident and demanded "stringent action against the perpetrators of the atrocity on the boys".
Last Sunday, to beat the scorching heat, the three young boys, aged around 12-14, jumped into a village well for a cool swim.
However, as some locals learnt of it, a large number of people, including many from upper castes, gathered near the well and pulled out the boys.
They were shouted at and subjected to abuses before some persons allegedly forced the boys to strip and paraded them nude around the village.Read | Maha driving India's growth story:Fadnavis to state expats in US
The boys can be seen wearing only sandals and some patvelia leaves, and they protested when at least one person was assaulting them on the legs and back with sticks and what appeared to be a leather belt.
After much cajoling, the boys and their families reluctantly lodged a complaint with the local police.
Several Dalit and political leaders from the opposition Congress and ruling Bharatiya Janata Party, including ex-minister Eknath Khadse, and other leaders from various parties, have condemned the incident and demanded that the culprits be booked under the SC/ST Act.
Former Chief Minister Ashok Chavan and former state Minister Laxman Dhoble, terming the incident as unfortunate, said that such incidents are on the rise in recent times and the matter has also been discussed in Parliament.
State Revenue Minister Chandrakant Patil, who is also the Guardian Minister of Jalgaon, said: "I have spoken to the Collector and Superintendent of Police.
Strict action will be taken in the matter including invoking sections of the SC/ST Act and Indian Penal Code, besides steps to ensure such acts are not repeated in future."
He said the well belongs to Ishwar Joshi, belonging to a nomadic tribe community and his servant Sonu Lohar had assaulted the boys.
Water Resources Minister Girish Mahajan said two persons have been booked under the provisions of Scheduled Castes & Tribes (Prevention of Atrocities) Act, Protection of Children from Sexual Offences (POCSO) Act and Information Technology Act, besides other charges for the incident.
Kamble and Mahajan said that from preliminary information received from the village, the boys had jumped into the well that was being used for drinking water purposes which earned the ire of the owners and the villagers.
Late this evening, the parents of the kids contended before TV channels that they (boys) were at fault as they failed to heed repeated warnings not to swim in that well and denied that they were under pressures to withdraw their complaints.Read | Five arrested for house-breaking thefts in Maha's Thane
Meanwhile, Gujarat legislator and Dalit leader Jignesh Mewani likened the Wakadi developments to the horrific April 2016 incident in his state's Una when some Dalit youth were similarly treated for skinning a dead cow.
"How can humans behave like this..Strictest action needs to be taken against the perpetrators, that's what we expect," Mewani told media persons.
People across the political and social spectrum expressed outrage over the incident and said it was regretful that it took place in Maharashtra which takes pride in great personalities like Chhatrapati Shivaji Maharaj, Mahatma Jyotiba Phule and Babasaheb Ambedkar.