Phyllis Chikundura, the spokesperson for Zimbabwe Anti-Corruption Commission, confirmed there was an ongoing investigation.
“We confirm there is such a report and there is such a probe,” she said.
Mrs Mugabe reportedly got the PhD after months of study in 2014.
State-run The Herald newspaper reported at the time that Mrs Mugabe’s dissertation was on the theme of “changing social structure (and) the functions of the family”.
It reported she undertook research on Zimbabwean children’s homes.
Mrs Mugabe was personally capped by her husband and then-president Robert Mugabe, who was also the chancellor of the University of Zimbabwe.
She was praised at the time by other government officials who defended the controversial degree award.
Mrs Mugabe had hoped to replace her husband as leader, but antagonised a faction of the ruling Zanu-PF party which led to a fallout within the party.
The military then stepped in and forced President Mugabe to end his 37 year rule of the southern African country and installing his former deputy, Emmerson Mnangagwa, as president.