Chief Minister Akhilesh Yadav late Thursday night appointed Principal Secretary (home) R.M. Srivastava as the inquiry officer in the case and called for a report within the next 15 days.
Another official of the home department will assist him.
Officials told IANS that in her response, submitted last week to the government, Nagpal had stuck to her earlier stand that she had done no wrong.
In her reply, Nagpal had also said that the boundary wall of the under-construction mosque at Kadalpur village in Gautam Budh Nagar was being built on Gram Sabha land and not on private land.
Officials said that authorities concerned had studied Nagpal's response after which the chief minister decided to order a fresh probe to "get to the bottom of the episode".
Nagpal was suspended as sub-divisional magistrate (SDM) July 27, attached with the state revenue board and served a charge sheet Aug 4.
The UP government in the charge sheet had accused her of taking a hasty administrative decision that lacked foresight and imperiled communal harmony in the region.