The resignation of 59-year-old Natarajan, Minister of State with independent charge of Environment and Forests, has been accepted by the President, a Rashtrapati Bhavan communique said.
It also said that Oil Minister M Veerappa Moily will hold additional charge of the Environment Ministry.
However, the surprise resignation triggered speculation whether her exit was related to the party work or due to reported complaints from industry that her ministry was holding up environmental clearances to projects.
Replying to the problem of environmental clearances delaying projects, Gandhi said, "This is what we face.... In India, there are lot of arbitrary powers. The Environment Minister or the Chief Minister can take any decision he wants."
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Natarajan, a senior member of Rajya Sabha in her third term, hails from Tamil Nadu and was brought into the ministry two years ago.
However, she maintained that she wanted to work for the party in view of the coming Lok Sabha polls and therefore she requested the Prime Minister to accept her resignation.
Sources said there could be some more ministers who could resign to be brought to party organisation in preparation for the elections.
Names doing the speculative rounds in this regard are Jairam Ramesh (Rural Development), Sachin Pilot (Corporate Affairs) and Jitender Singh Bhanwar (MoS-Defence).
In the wake of the rout in Rajasthan Assembly elections, Pilot's name is being talked about as a possible PCC chief.
There is also talk of a reshuffle in the AICC in which some general secretaries may be dropped. Bhanwar, considered close to Rahul Gandhi, is a possible candidate for general secretaryship in the AICC. He had earlier been an AICC Secretary.