Gupta, who was appointed to the body governing higher educational institutes barely a year ago, resigned on health grounds.
The sources, however, maintained he had developed differences with Prakash and was unhappy with the chairman's style of functioning.
Gupta is understood to have announced his decision to the bureau heads of the organisation yesterday.
Before joining UGC, Gupta was working as head in the Climate Change Programme Division of Department of Science and Technology.
During his brief stint, Gupta, a scientist, was instrumental in introducing e-governance system in the organisation, made the affiliation process transparent and also introduced the 'integrated financial division'.
UGC was the first autonomous body to have such a system.
The latest development also comes in the backdrop of the HRD Ministry sacking UGC member Yogendra Yadav couple of months back for joining the Aam Aadmi Party.
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