The son eventually committed suicide before his father could reach home.
The charge with Sahay was today handed to the additional chief secretary, finance, D K Jain, sources said.
The employee unions have been demanding registration of FIR against Sahay. Class four agriculture department employees association has also threatened a sit-in at the office of the commissioner of agriculture, Pune, from September 7.
"For now he has been divested of his charge," the official added.
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According to Rajesh Ghadge, joint secretary, agriculture department, on the afternoon of August 12 he got a call from his 23 years old son who was suffering from depression. The son asked him to return to their house in Navi Mumbai at the soonest, failing which he said he would end his life.
Ghadge requested Sahay to let him go home early, but Sahay allegedly refused. A distraught Ghadge again pleaded with him as he got another call from his son, but in vain.
Agriculture Minister Pandurang Phundkar had yesterday said he had ordered a departmental inquiry into the incident.
President of class four employees association of agriculture department, Bhausaheb Pathan, demanded that the probe be completed in time and Sahay be transfered immediately.
Senior Shiv Sena leader and MLC Neelam Gorhe expressed concern that such an incident had happened in Mantralaya, the Government headquarters, and called for a humane response by the administration in such circumstances. She also demanded in-depth inquiry into "high-handed" behaviour of senior officials.