Sources said Meghwal briefed Singh about the case and is understood to have been assured of party's support as charges have not been proved yet.
Singh is said to have advised the Minister of State for Chemicals and Fertilisers to stay away from media to avoid any controversy, they said.
Meghwal, 42, is the only representative from Rajasthan in Narendra Modi's council of ministers. He was named in an FIR filed in 2011 by a woman who alleged that her husband repeatedly drugged her and then allowed his friends, among them Meghwal, to rape her.
Rajasthan Police had, in 2012, closed the case saying the charges were false and fabricated. The woman had then approached a district court which, too, dismissed the charges.
She filed a review petition, following which additional district judge issued notices to Meghwal and 17 others in this case last week, asking them to respond by August 20.
National Commission for Women Mamta Sharma has demanded that the Prime Minister sack Nihalchand.
The Congress and its women workers also held a protest in Delhi on Wednesday demanding action against the Minister.