The incident took place at Janakipeta in Amalapuram town of the district in Andhra Pradesh.
According to police, after the cow died following electrocution, its owner, a farmer, engaged the two Dalits, who were brothers, for skinning the animal before it was buried.
On getting to know of the skinning, the "gau rakshaks" (cow vigilantes) went to the place and beat up the duo, identified as Mokati Elisha and Lazer, suspecting that they had killed the animal.
The two were admitted to a hospital in Amalapuram for treatment and Elisha's condition was said to be serious.
"We have registered a case under SCs/STs (Prevention of Atrocities) Act against some persons, who are yet to be identified. We are investigating the case and gathering clues about the suspects," a police official said over phone from Amalapuram.
The incident has taken place when the flogging of a Dalit family at Una in Gujarat last month created a countrywide uproar over cow vigilantism.
Three days back, Prime Minister Narendra Modi, in his first public denouncement of cow vigilantes, had said that he felt enraged at such "anti-social elements", who indulged in crimes by the night and masqueraded as cow protectors by the day.
A day later in Telangana, Modi had asked people to beware of "fake" cow protectors as they were trying to create "tension and conflict" in the society and said that "if you have to attack, attack me" but stop attacking my Dalit bretheren".