During the Lok Sabha election campaign, Thakur had described Godse as a patriot, triggering a huge political storm.
This is the second time Ms Thakur has called Nathuram Godse a "patriot" - she first made the same comment in May.
Taking strict cognizance of her controversial remark, BJP working president JP Nadda on Thursday condemned Thakur's statements and said that the party does not support or endorse her views. Nadda said she will not be allowed to participate in parliamentary party meetings in the Winter Session.
MP Sadhvi Pragya Singh Thakur might be sacked from the party membership over her comments in the Lok Sabha where she hailed Nathuram Godse, the assassin of Mahatma Gandhi, according to Zee Media sources.
BJP ally Janata Dal (United) welcomed the ruling party's action against Thakur but its spokesperson KC Tyagi demanded that the matter should be referred to Lok Sabha's ethics committee, highlighting that many members, including former Prime Minister Indira Gandhi, had been expelled on its recommendations in the past. "Truth is that I did not tolerate insult to Udham Singh yesterday", the Bhopal MP tweeted.
The BJP's move to drop her from the consultative committee of MPs on defence comes against this background. "BJP never supports such a statement or ideology". People should not be swayed by this storm.
During a debate on the Special Protection Group (Amendment) Bill on Wednesday, when Dravida Munnetra Kazhagam (DMK) MP A Raja was speaking on the Bill, Thakur apparently referred to Godse.
"We condemn any philosophy which describes Nathuram Godse as a patriot".
Opposition parties attacked Prime Minister Narendra Modi, saying his "inaction" against her proves his latent support to "Godse's sinister thought". "Those who call him a terrorist should look within, and they will get a reply in this election", she had said.
Thakur created a controversy on Wednesday with her remark in the Lower House during DMK member A Raja's narration of a statement by Nathuram Godse before a court on why he killed Mahatma Gandhi.
Back then, the BJP had immediately gotten into damage control and distanced itself from Thakur's statement, while also asking her to tender a public apology. "But in my heart, I can not forgive her", PM Modi had said. Several leaders raised had raised objections, pointing that Pragya is an accused in the 2008 Malegaon blast case, and that she is facing trial for charges under the Unlawful Activities (Prevention) Act.