Patel, who was questioned on Monday and Tuesday for over 17 hours, skipped the questioning after sending a letter to the agency through his advocates.
The Nationalist Congress Party (NCP) leader had skipped ED questioning on June 6 too, citing prior appointments.
The ED said it will issue a fresh summons to Patel.
The case follows a criminal complaint registered by the ED over alleged irregularities in fixing air slots for other international airlines that purportedly caused losses to Air India.
Patel, who has denied any wrongdoing, was the Civil Aviation Minister in the United Progressive Alliance (UPA) government between 2004 and 2011 when Air India and Indian Airlines merged.
The ED investigation covers the merger, purchase of 111 aircraft from Boeing and Airbus for Rs 70,000 crore, ceding of profitable routes and schedules to private airlines as well as opening of training institutes with foreign investment.
The ED has questioned several Air India officials and recorded statements of the then Civil Aviation Secretary and others.
In its May 1 chargesheet, the ED alleged that corporate lobbyist Deepak Talwar finalised various communications addressed to Patel on behalf of Emirates and Air Arabia.
Talwar, now in judicial custody, was extradited to India from the United Arab Emirates (UAE) in January this year.
It is also investigating how money received in Talwar's bank accounts was moved to government employees in India including those in the Civil Aviation Ministry.
( With inputs from IANS )