The supporters of Thopte have written to interim Congress president Sonia Gandhi and Rahul Gandhi, while some have shown a rebellious attitude towards the party.
Sources say that senior Congress leader Mallikarjun Kharge will be talking to these people to quell a Karnataka type rebellion within the party.
Other MLAs who have not gone public have listed their grievances before the party. Some of the MLAs have said that they will meet Sonia Gandhi and Rahul Gandhi to apprise them of the situation.
While the intervention from New Delhi has yielded results as Praniti Shinde has denied any differences with the party and Sangram Thopte has said that he is with the party.
Earlier on Tuesday, Congress ministers accompanied by Mallikarjun Kharge, K.C. Venugopal and party secretary Ashish Dua, met Sonia Gandhi and Rahul Gandhi and apparently talked about the dissent.
Senior ministers, including Balasaheb Thorat and Ashok Chavan who took oath on Monday, also met the top leadership.
The Congress in the state has been facing internal differences with some senior leaders saying that they have been ignored in the cabinet expansion.
Amin Patel, the two time MLA from Mumbai, was expecting a cabinet berth, but was overlooked while younger members Aslam Sheikh and Varsha Gaikwad were inducted in the cabinet. In Mumbai, former minister Arif Nasim Khan who narrowly lost the election is also believed to be upset. Now he has demanded that the Maharashtra Government follow Kerala and pass an anti-CAA resolution.
The senior leaders have made their grievances known to the party leadership. The Congress, which came fourth in the Assembly polls, is now planning to accommodate senior leaders in the party and many may be assigned organisational work, said a source.
The Congress has got 12 berths in the cabinet and is eyeing some key portfolios. Apart from the Speaker's post, the party has to appoint a new state president as Balasaheb Thorat has been inducted in the cabinet.
Former chief minister Prithviraj Chavan, who was the frontrunner for the Speaker's post, is now being tipped to be the next state Congress chief. Another former chief minister Ashok Chavan is now part of the Uddhav Thackeray cabinet.
( With inputs from IANS )