Tharoor was quizzed for over four-and-a-half hours at the Anti Auto Theft Squad (AATS) office in South Delhi in two sessions.
In the afternoon session, Tharoor's driver Bajrangi was also quizzed along with the Congress MP.
Sources said that Tharoor faced tough questions on the IPL controversy which had broken out in early 2010 when he was minister of state for external affairs.
Tharoor first reached Sarojini Nagar police station and however, was later taken to the office of AATS in Vasant Vihar in south Delhi around 11.30 AM where he was questioned by a five-member SIT team.
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Delhi Police had earlier examined the former minister on January 19.
Sources in the police said the SIT team also questioned Sanjay Diwan, a common friend of both Tharoor and Sunanda, Rajat Mohan (cardio of Ganga Ram Hospital), Tharoor's domestic help Narayan Singh and his PA Praveen Kumar.
DCP Mangesh Kashyap from the Economic Offences Wing (EOW), who was also part of the team, also asked some questions to Tharoor about the now defunct IPL Kochi franchise.
He was questioned about the circumstances in which Sunanda had left him at the airport after returning from Thiruvananthapuram to Delhi on January 15 and checked in at Leela Hotel, the sources said.
The police team probing the case has so far questioned at least 15 people. Tharoor, his staff members and close friends were among those quizzed by Delhi Police.
Sources said that during the questioning of Menon, some new inputs emerged and Tharoor's response on them were required for the ongoing probe.
Meanwhile, Police Commissioner B S Bassi said that SIT has questioned almost all persons, who were required to be quizzed, in the case and if there is need, police will also question some more persons.
"Our aim is to verify the fact to establish the truth," Bassi told reporters here.