The statement has been considered by the party to be mocking Prime Minister Narendra Modi's pet project Swachh Bharat Mission, according to internal sources.
She was summoned to the party headquarters in Delhi were she met Nadda and Bharatiya Janata Party (BJP) organisational general secretary B.L. Santosh and was asked to refrain from making statements that go against the party's programmes and ideology.
Thakur, an accused in the 2008 Malegaon bomb blast case who is currently out on bail, did not say anything to the media after her meeting.
On Sunday, she had said: "We have not been elected to clean your drains or toilets. The work which we are supposed to do and are elected for, we will do it honestly. This we had said in the past, saying it today and stick to it in future as well."
Thakur is known for kicking up new controversies since she joined the BJP in April, ahead of the Lok Sabha polls.
Just days after joining the party, she claimed that Maharashtra ATS chief Hemant Karkare who was killed in the 26/11 Mumbai terror attacks died due to her "curse" as the police "tortured" her when she was in the custody for the 2008 Malegaon bomb blast case.
The BJP had distanced itself from the comments saying it was her personal view. Later, she apologised for her statement.
During the Lok Sabha poll campaign, she called Nathuram Godse the assassin of Mahatma Gandhi a "patriot".
Later, she apologised after the party did not support her remarks and Modi even said he would not be able to forgive her despite the apology.
( With inputs from IANS )