Mr Malik said these MLAs will be back in the party soon.
The NCP on Sunday night claimed three MLAs, who among others had attended swearing-in ceremony of Ajit Pawar as deputy chief minister on Saturday, were flown to Delhi in a chartered plane by the BJP the same day.
NCP chief spokesperson Nawab Malik said the three MLAs have said that they are with the party.
He said while Daulat Daroda and Nitin Pawar have sent video messages saying they are with the NCP, another MLA Narhari Zirwal's message was shared on the twitter handle of the NCP.
Mr Daroda, Mr Pawar and Mr Zirwal represent Shahapur, Kalwan and Dindori assembly constituencies, respectively.
"Daulat Daroda, Nitin Pawar and Narhari Zirwal were taken to Delhi by the BJP in a chartered plane yesterday," Mr Malik said, adding that "Pawar and Daroda have sent us their video messages saying they are with the party".
Earlier in the day, Mr Malik said that apart from the three MLAs, Babasaheb Patil (Ahmedpur), Anil Patil (Amalner) were reported ''missing''.
While Anil Patil tweeted that he is with the NCP, video messages of Babasaheb Patil, Mr Pawar and Mr Zirwal were shared on the twitter handle of the NCP.
Mr Malik said these MLAs will be back in the party soon.
Mr Malik had taken to Twitter and tagged Anil Patil's tweet in which the latter said he continues to be part of the NCP and expressed faith in the leadership of Sharad Pawar.
In the tweet, Mr Patil said he went to the Raj Bhawan since Ajit Pawar was the legislature party leader.
"I wasn't aware about what was going to happen at the Raj Bhawan. I am with Sharad Pawar," Mr Patil said in the tweet. Earlier on Saturday, Mr Daroda's family filed a missing person complaint with police.