The Kadapa MP was brought to CBI office in Kendriya Sadan at 10.30 AM amid tight police security.
Jagan, who was arrested by the agency on May 27 in the disproportionate assets case, is under judicial remand till June 11 and lodged at Chanchalguda Jail.
The High Court had yesterday given Jagan's custody to the CBI for two days till June 10 and directed the agency to question him during the day in presence of his lawyers.
The CBI had sought the custody of Jagan, saying it needed to confront him over the facts emerging out of the investigation into the Vodarevu and Nizampatnam Port and Industrial Corridor (Vanpic) project.
The agency also informed the court that the accused did not cooperate with the agency during his last 5-day custody that ended on June 7.
The central probe agency wanted Jagan's custody to verify the alleged investments of Rs 850 crore made in his businesses as part of quid-pro-quo transactions.
The CBI also sought to gather information on alleged transfer of funds from different companies and countries that finally reached the firms owned by Jagan.
It so far filed three charge sheets in the case and has accused Jagan of getting investments of several crore rupees from firms into his own businesses when his father late Y S Rajseskhara Reddy was the Chief Minister of Andhra Pradesh.
According to the FIR filed by CBI in August last year, the Jagan-owned Jagati Publications Pvt Ltd that runs Sakshi daily was incorporated on June 14, 2006 and accumulated business losses of Rs 350 crore in four years.