Mahila Congress workers also staged a protest outside BJP headquarters demanding resignation of the 43-year-old Minister of State for Chemicals and Fertilisers.
Congress spokesperson P C Chacko said, "It is a shame for the government that a person, who is accused of a heinous crime like rape and has been summoned by the court, still continues in the government.
"Now they (the government) say they will follow the legal course. This is too much.... The minister should not be allowed to continue even for a moment", he said.
He added that the government should act on moral grounds in this case and not politically.
BJP, however, defended Nihalchand, saying "there is nothing substantial against him" and that he was being "falsely implicated" while terming the charges against him as "politically motivated".
"He (Nihalchand) has been exonerated by the authorities during the previous Ashok Gehlot government in Rajasthan after nothing has been found against him. The police is reinvestigating the matter and he is cooperating.
"As long as there is nothing substantial against him, we cannot take action against him," BJP Spokesperson Meenakshi Lekhi told PTI.
Nihalchand on his part refused to comment on the controversy involving him in the rape incident as alleged by the survivor. "No comments," he said when asked about the allegations against him.
Lekhi said just as it is wrong to indulge in activities as alleged by the woman, it is equally important that nobody can be falsely implicated either or harassed like that. "A balance has to be maintained," she said.
She said today the rape survivor has come up with fresh facts which she did not come up with earlier and unless the other version is heard no action can be taken against him.
Lekhi said "this was being done on purpose by his political opponents. It seems to be politically motivated. Politicisation of legal process is not permissible under the law."
Targeting Modi, Mahila Congress President Shobha Oza said he talks of zero tolerance in matters of crime against women but "when the name of one of his ministers surfaces, neither the minister puts in his papers nor the prime minister demands it."
She alleged that the victim from Rajasthan is being intimidated and as long as the minister remains in the post, there will be pressure on her.
Nihalchand and 16 others were named in an FIR lodged by a 24-year-old married woman from Jaipur. In the FIR filed in 2011, she alleged that he had sexually exploited 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.
Nihalchand and the other accused have now been asked by a Jaipur court to appear before it in connection with the case after a review petition was filed by the complainant.
Nihalchand is the only MP from Rajasthan in Modi's Cabinet.
Congress guns for ouster of Modi's minister accused of rape
Governor row: Cong attacks govt; JD-U wants debate
PM should sack minister named in rape case: Women's panel
Festive atmosphere in Lok Sabha as members take oath
BJP spokespersons who missed out on ministerial posts