The incident occurred on Sunday but came to light only after videos of the boys walking naked in the Vakadi village found its way into social media.
Maharashtra Social Justice Minister Dilip Kamble told journalists that two people have been arrested in connection with the incident and further investigations are underway.
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 to 14, jumped into a village well for a swim.
However, as some locals learnt of it, a large number of people, including many from so-called upper castes, gathered near the well and pulled out the boys.
They were shouted at and subjected to abuses before some people allegedly forced the boys to strip and paraded them nude around the village.
The boys can be seen wearing only sandals and some tree leaves in the video, and they protested when at least one person was whipping them on the legs and back with sticks and what appeared to be a leather belt.
After reluctantly filing a police complaint, the boys and their families now face intense pressure from influential villagers to take it back, reports said.
Several Dalit and political leaders from the opposition Congress and ruling Bharatiya Janata Party, including ex-minister Eknath Khadse, Gujarat Dalit leader Jignesh Mewani, have condemned the incident and demanded that the culprits be charged.
This evening, Maharashtra Minister Chandrakant Patil promised stern action besides steps to ensure such acts are not repeated in future.