Deputy Commissioner of the centre Sher Singh Luhadia and in-charge R K Sharma were suspended after a review meeting held by Chief Minister Vasundhara Raje.
Raje directed officials to improve the condition at the Hingonia Cow centre and make arrangements for its better management.
She also ordered a high-level inquiry into the matter.
UDH Minister Rajpal Singh, Animal Husbandry Minister Prabhu Lal Saini and senior officials visited the 'gaushala' and apprised the chief minister about the situation before her departure to Delhi.
Congress has alleged that 100 cows have died due to "mismanagement and lack of facilities" at the gaushala while VHP claimed that more than 500 cows died due to the "inhuman behaviour" of Raje government towards them.