Official sources said Goswami who turned 60 last month and would have continued till June 30 was asked to resign after which he submitted his resignation.
The sources which earlier said Goswami was removed later conveyed to the media that he was allowed to resign to give a "dignified" exit.
The names of Rural Development Secretary L C Goyal, a 1979-batch IAS officer of Kerala cadre, and Petroleum Secretary Saurabh Chandra, 1978-batch IAS officer from UP cadre, are doing the rounds as Goswami's successor.
This is the second instance of the removal of a top bureaucrat in a week after Foreign Secretary Sujatha Singh's services were curtailed last Wednesday after she refused to resign from the post. While there were no allegations of impropriety against her, the Government is said to have been unhappy with her leadership of the Ministry.
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The continuance of Goswami became untenable after he had admitted to Home Minister Rajnath Singh that he had spoken to CBI officials before they arrested Sinh in Kolkata on Saturday.
Rajnath Singh who had returned to the capital yesterday talked to Goswami who admitted to have called up CBI officials probing the Saradha scam in connection with Sinh's arrest.
The Minister immediately briefed the Prime Minister on the issue last night. Today he called Goswami for a discussion followed by a meeting with CBI Director Anil Sinha.
Both the officials maintained silence on their separate meetings with the Home Minister.