Official sources said the four-member team from Mumbai began questioning Singh at Raj Nivas, five days after an ED team from Chennai had set the motion in process.
The ED's questioning comes after the Prime Minister's Office gave a green signal to the Directorate to go ahead with recording Singh's statement on his recommendation as a Congress Rajya Sabha member in 1997 for expeditiously issuing passport to Khan, a Pune stud farm owner.
Singh was embroiled in controversy after his name cropped up during the questioning of Bihar-based Congress leader Amlendu Pandey over the issue.
The Lt Governor has admitted to have recommended expeditious issue of passport to Khan, but claimed he never knew him.
In a letter to Home Minister P Chidambaram last week, Singh had claimed he asked for the passport to be granted on humanitarian grounds because he had been told that Khan needed to travel abroad urgently to visit his ailing brother.