Rains in the city filled the cattle protection centre, run by the Society for Prevention of Cruelty to Animals (SPCA), with slush and led to poor sanitary conditions, leaving the cattle in a hapless situation, officials said.
The SPCA, however, denied any negligence on their part.
Joint Director of Animal Husbandry V Venkateswara Rao said rains and slush caused pneumonia, leading to the death of cows.
"There were also some starvation that contributed to the death (of 46 cows). We have opened a special camp to treat the other cattle in the centre and the situation is now under control," he added.
While the centre could accommodate only about 150 cattle, 480 were housed there in crammed conditions, the officials alleged.
District Collector Kartikeya Mishra ordered an inquiry into the cattle deaths and disbanded the society. He constituted a committee, headed by the local Revenue Divisional Officer (RDO), to manage the cattle shelter.
The RDO, Raghu Babu, who visited the centre, said there was negligence on part of the society members that led to the tragedy.
On the instructions of the collector, the Sarpavaram police registered a case of negligence against the SPCA members but no arrests have been made yet.
The SPCA members, led by its president R V M R Rao, met Mr Mishra last night and blamed rains in the last few days for the cattle deaths. They claimed there was no negligence on their part and they fed the cattle properly.
They demanded that the case against them withdrawn.
The collector, however, said the remaining cows in the centre would be given to the Integrated Tribal Development Agency, Rampachodavaram.
The cattle would reared by the local farmers, he said.