PM Modi has asked him to continue for two weeks, principal government spokesperson Sitanshu Kar said.
Former cabinet secretary P K Sinha has been appointed as officer on special duty by the Prime Minister, he said.
Misra has been with PM Modi in the PMO since 2014.
In a Tweet, PM Modi said: After serving the PMO assiduously and diligently for over five years and making an indelible contribution to India’s growth trajectory, Nripendra Misra Ji will be embarking on a new phase of his life. My best wishes to him for his future endeavours.
Nripendra Misra is among the most outstanding officers, who has a great grasp of public policy and administration. When I was new to Delhi in 2014, he taught me a lot and his guidance remains extremely valuable.