The find was revealed by Phan Ho, the director of the management board of the heritage site, on May 28.
The monolithic sandstone Shiv Linga, which is 2.24 x 1.68 metres in size, is the largest of its kind unearthed in Vietnam to date, according to experts.
The head of the conservation group, Jalihal Ranganath, said the discovery is helpful for the restoration of the Cham temple.
Vietnamese and Indian experts have also completed the restoration of four stone pillars in front of Tower A10 worshipping God Shiva.