"Dr Venugopal has not resigned and he continues to perform his duties as Director, Indian Museum. He is on deputation for three years," a statement issued by the museum said.
It clarified that no spokesperson of the institute had earlier given a statement saying that he is resigning as reported in a section of the media.
Venugopal, whose tenure has been embroiled in controversy for alleged neglect of museum artifacts, had joined Indian Museum in October 2013.
Eyebrows were also raised after senior museum official Sunil Upadhyay went missing.