The academy is coming up at a cost of Rs.600 crore on 500 acres of land at Palasamudram in Gorantla mandal of Anantapur district.
Jaitley said the academy would create employment opportunities in the district and hasten the process of development in backward Rayalaseema region.
He said the drought-prone district had huge development potential due to its proximity to a metro city like Bengaluru.
Chief Minister N. Chandrababu Naidu said the academy will train probationary customs and excise officials.
It is the second academy of its kind in India and the first in South India. At present, NACEN is located at Faridabad in Haryana, which is also the regional training centre of the World Customs Organisation for South Asia.
NACEN is one of the higher education institutions promised by the central government in Andhra Pradesh Bifurcation Act 2014.
Jaitley assured Andhra Pradesh that all promises made in the act including construction of Polavaram project would be fulfilled.
Central minister M. Venkaiah Naidu said the central government was extending all possible help to the state. He said Indian Institute of Technology (IIT) was coming up at a cost of Rs.2,200 crore while the Indian Institute of Science Education and Research (IISER) was being built with an estimated cost of Rs.1,200 crore in Tirupati.
Foundation has already been laid for Indian Institute of Management (IIM) coming up in Visakhapatnam at a cost of Rs.900 crore, he added.
Venkaiah Naidu said School of Architecture would be established in Vijayawada, Indian Culinary Institute in Tirupati, National Institute of Technology (NIT) in Guntur, Petroleum University in Rajahmundry and a central university in Anantapur district.
Chandrababu Naidu mooted a Hyderabad-Bengaluru industrial corridor and urged Jaitley to approve it. He also sought all assistance from the central government to ensure that the state develops at par with neighboring states.
He vowed to complete Polavaram project in four years. He said the government would irrigate drought-prone Rayalaseema region by linking Godavari, Krishna and Penna rivers.