Photos, some shared by the state's opposition Congress, show a large group sitting in a room in their underwear. The farmers are also seen leaving a police station, their clothes bundled in their arms.
The group had gathered at a government office to present a list of demands to the district administration. The state's ruling BJP says the protest was organised by the Congress.
When the protest turned violent, the police allegedly used batons, teargas and water cannons. The farmers allege that they were finally detained at the police station, beaten up and forced to strip.
The police, however, claim their men were injured in stone throwing by the farmers.
Chief Minister Shivraj Singh Chouhan said his government "cannot tolerate violent protests" and accused the Congress of trying to stir trouble.
"The Congress unnecessarily created a situation in which lathis and stones were used and vitiated the atmosphere," Mr Chouhan told reporters. On the stripping charge, he said he had asked for a report.
State home minister Bhupendra Singh said he had asked the police chief to investigate whether the farmers were forced to strip or they did it voluntarily.
"It was a congress campaign and there was stone-throwing. We have heard about the stripping, we are waiting for an inquiry report. We need to know whether the allegation is political and whether the police disrobed them or the farmers stripped in protest," said state home minister Bhupendra Singh.
Bundelkhand, one of the country's most parched regions, has seen aggressive farmer protests and demands for loan waivers recently after a long spell of drought and failed crop. In June, five farmers were killed in police firing during protests.