The police say they have no role in the matter and they cannot get the cows released from the private trust headed by a local politician. The farmer has now approached the district administration, which has ordered an inquiry into the matter.
The cows, let out to graze on October 3, never came back, alleged the 45-year-old farmer.
"The villagers were involved. They took away the cows in presence of the police," said the farmer, who is now doing his best to take care of five young calves. "I am a poor man. We are farmers. We sell milk and earn a living. It has been 11 days since my cows were taken away," he said.
"We sold 1 quintal of milk per day... now how do you expect me to feed my children?" added his wife Razia.
Denying allegations of providing support to the villagers, local police officer Chand Singh Rathore said his men had been sent to control the crowd.
Mr Khan, the police said, has not filed a complaint, but still an investigation is on.
There is no written complaint against Subba Khan either, despite the allegations of cattle smuggling. But the police say they can't get his cows released. "The villagers got the cows deposited (in the cow shelter), not us," said Mr Rathore. "We don't have any report in this matter. Now they are saying it is their cows. We are saying we did not seize them and neither can we have them released," the officer said.
Alwar had occupied headlines in April after a 55-year-old dairy owner was beaten to death on suspicion of cattle smuggling. The video footage of Pehlu Khan being yanked by the neck, thrown to the ground and kicked by cow vigilantes had sparked nationwide outrage.
Months later, the Rajasthan police has given clean chit to the six men he named as his attackers in his dying declaration, saying there was no evidence against them.