Police said eight persons were arrested for involvement in the attack but clarified that the incident was not linked to cow vigilantism.
The incident occurred on Monday night in Amalapuram town of East Godavari district.
Mokati Elisa and his brother Lazar were stripped, tied to a tree and thrashed when they were seen skinning a dead cow in a graveyard.
The victims sustained injuries on heads and other parts of the body.
A police officer said the eight persons were looking for their missing cow and they alleged that the duo killed and skinned their cattle.
Chief Minister N. Chandrababu Naidu took serious note of the incident and asserted that nobody would be allowed to break law and order of the state.
A series of attacks on Muslims and Dalits by “gau rakshaks” (cow protectors) in recent months in different parts of the country has triggered outrage.
Prime Minister Narendra Modi has also condemned the attacks, saying fake “gau rakshaks” were behind these incidents.
He said anti-social elements were masquerading as “gau rakshaks”.
The centre on Tuesday ordered state governments to ensure that no local groups are allowed to initiate acts of violence using cow protection.