Singh had put in his papers last week claiming that the special court in Mumbai had pointed fingers at him while discharging BJP President Amit Shah on the ground that the CBI case in Sorabuddin fake encounter killings was "politically" motivated.
When contacted, Press Secretary to the President Venu Rajamony said "the President has accepted his resignation."
His resignation has fuelled speculation whether it has anything to do with the proposed move of Enforcement Directorate to register a case against Qureshi for alleged violation of FEMA.
Singh's trouble started early last year after his name was linked to Qureshi, who was facing cases of Income Tax department for alleged alleged hawala funding and tax evasion.
Singh and his wife had been served an Income Tax notice last year asking them to give details about their credit card transactions and recently he was asked to submit his property details.