The handover was made at the PTDI facility in Bandung, in West Java province on the island of Java, The Jakarta Post reported.
Defense Minister Purnomo Yusgiantoro said the aircraft will be used to patrol for people-smuggling boats carrying illegal migrants headed for waters around Australia's Indian Ocean territory of Christmas Island.
The navy operates the smaller NC-212 MP aircraft, also made by PTDI at its facility in Bandung, the Post said.
PTDI President Budi Santoso said the order showed the trust in and support for the manufacturer's products.
"We have replied with hard work and commitment by producing quality aircraft that are on time and on budget," Budi said.
The Post also reported Purnomo said the ministry needed at least 54 NC-212s and 21 CN-235s, while Adm. Marsetio, the navy's chief of staff, said the aircraft would be procured by 2024.
PTDI will deliver the next CN-235 in December and the third aircraft in February next year.
The Indonesian Ministry of Defense signed the $80 million deal in December 2009 off the back of a strategic planning review.
Spanish aircraft maker EADS CASA -- Construcciones Aeronauticas SA -- and PTDI formed a joint venture, Aircraft Technology -- AirTech -- to develop the CN-235 aircraft in two variants for civil and military use. The original design was for military transport and as a regional airliner.
A report in Defense Industry Daily at the time of the signing in 2009 said the aircraft will be fitted with Thales' AMASCOS mission control system.
AMASCOS subsystems include Thales/EADS Ocean Master Mk II search radar, thermal imaging from Thales, Elettronica's ALR 733 radar warning receiver and CAE's AN/ASQ-508 magnetic anomaly detection system.
The aircraft also comes with either MBDA's AM-39 Exocet missiles or Raytheon's Mk 46 light torpedoes.
The high-wing aircraft has two General Electric CT&-9C3 turboprop engines and Trimble TNL7900 Omega global positioning system and a Northrop Grumman-built LN92 ring laser gyroscope inertial navigation system.
The first flight of the CN-235 was in 1983 with first operational use in 1988. The main buyer has been Turkey, picking up 61 aircraft. Other buyers of large numbers have been the air forces of Spain and the Republic of Korea.
In March last year, the South Korean coast guard received its fourth and last CN-235 ordered from PTDI.