She has been transferred from the Mumbai municipal corporation to the water supply department in Mantralaya.
The bureaucrat has also been issued a show-cause notice by the Maharashtra government for the 'sarcastic' tweet, the official said.
The action against Choudhari follows the demand by Nationalist Congress Party president Sharad Pawar who on Sunday sought "exemplary" action against the IAS officer for her controversial tweet on Gandhi.
In a letter addressed to Maharashtra Chief Minister Devendra Fadnavis, Pawar had said, "If the government doesn't take action it would be deemed that its policy and intention has reached its lowest ebb".
In the tweet, which has since been deleted, Choudhari, deputy municipal commissioner of Mumbai, had called for the removal of Mahatma Gandhi's statues from across the world and his images from the Indian currency notes. She also "thanked" Mahatma's assassin Nathuram Godse for "30.1.1948", the day Gandhi was killed.
After a row erupted, the officer clarified the tweet was "sarcastic" and that it was "misinterpreted".
"A government official in a progressive state like Maharashtra making such insulting comments against Mahatma Gandhi, and the state government turning a blind eye to it is a serious matter," Pawar had said.
Her comments were not only condemnable but were fit for action against her, the former Union minister had said, adding that he was shocked to hear about the contents of the tweet.
Pawar had said he expected an "exemplary action" against the bureaucrat from the chief minister. The Congress and NCP had demanded the suspension of Choudhari over the tweet.
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