Natarajan was appointed chairperson of the Congress' manifesto committee, while Gautam was made a member of the party's state coordination committee.
Several of her supporters, including Congress MLA from Mandsaur's Suvasra constituency, Hardeep Singh Dang, and party's district vice president Mahendra Gurjar also resigned from their respective organisational posts.
Natarajan refused to comment on the issue when contacted. "I would not make any public statement on the party's internal issues," she told news agency PTI.
Notably, Gautam had during the 2009 Lok Sabha polls rebelled against the Congress when Natarajan was chosen as the party nominee from Mandsaur.
The development comes ahead of Congress president Rahul Gandhi's visit to Mandsaur scheduled on June 6, the first death anniversary of six farmers who were killed at a village here in police firing during a protest last year.
Congress has so far been able to keep all the disparate factions of the party united ahead of the polls. The recently announced appointments in the state unit were seen as a bid to appease all top leaders of the state.
The party had named Digvijay Singh as the coordination committee chief of Madhya Pradesh on Tuesday. Earlier, the party had appointed Jyotiraditya Scindia as campaign committee chief and Kamal Nath as Madhya Pradesh Congress Committee (MPCC) president.
The three leaders are said to be eyeing the chief ministerial post in the state and it will be interesting to see as to how the party deals with their ambitions ahead of the assembly polls.
With Agency inputs