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.
The exit of Goswami, a UPA government appointee, came on a day of hectic activities following media reports that he had tried to prevent CBI officers from carrying out Sinh's arrest on Saturday.
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.
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.
It was reported on Sunday that CBI was miffed with the interference by Goswami in the arrest of Sinh. The agency had submitted a report to the PMO on the issue about Goswami and a Joint Director level officer of CBI.
Rajnath Singh talked to Goswami who admitted to have called up CBI officials probing the Saradha scam in connection with Sinh's arrest.
Home Minister immediately briefed the Prime Minister on the issue on Tuesday night. On Wednesday 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.
Goswami, a 1978-batch IAS officer of Jammu and Kashmir cadre, was appointed as Home Secretary in 2013 during the tenure of UPA Government. He was said to have been close to Matang Sinh, a controversial politician from Assam who was a Minister of State for Home in PV Narasimha Rao's government.

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