Both Lion Air and national carrier Garuda, which operate the American-made aircraft, were issued notices to conduct the inspection immediately, Transportation Minister Budi Karya Sumadi said yesterday.
"The results of the inspection will be handed over to KNKT to assist with their investigation," said Mr Budi, using the Indonesian abbreviation for the National Transportation Safety Committee.
Lion Air is believed to have a fleet of eight Boeing 737 Max 8 aircraft, while Garuda has one.
Boeing said yesterday it was deeply saddened by the loss of the Lion Air flight and will be providing technical assistance "at the request and under the direction of government authorities investigating the accident".
"We extend our heartfelt sympathies to the families and loved ones of those on board," said the aircraft manufacturer in a brief statement.
The government's order came a day after Flight JT610 plunged into the Java Sea minutes after take-off from Jakarta's Soekarno-Hatta airport.
TRYING TO LOCATE BLACK BOX
We are still searching for the fuselage. Usually, the black box wouldn't be far from the fuselage. We started at 10.30am… using multi-beam echo sounders. We have not picked up any sign of a large object on the sea floor.
NATIONAL SEARCH AND RESCUE AGENCY CHIEF MUHAMMAD SYAUGI
Efforts to locate survivors and the black box flight recorder in the waters off Karawang, West Java, continued into a second day yesterday.
The plane had lost contact with air traffic controllers at the Soekarno-Hatta airport 13 minutes after it took off at 6.20am local time (7.20am Singapore time) on Monday.
The flight, which was scheduled to arrive in Pangkal Pinang, in Bangka Belitung Islands province, at 7.20am, vanished from radar about 10 minutes after the pilot requested, and was granted, permission to "return to base".
Mr Budi, while giving his assurance that a thorough and objective investigation will be carried out, said KNKT investigators are now looking at the pilot's request to return to base.
"But before we examine the crew's actions and consider the possibility of human error, we must first perform an analysis of the plane," said Mr Budi.
The minister was speaking to reporters after accompanying President Joko Widodo on his visit to the Jakarta International Container Terminal, where a command centre for the search and rescue operations had been set up.
According to National Search and Rescue Agency chief Muhammad Syaugi, rescuers have recovered and sent 34 body bags containing human remains, including possibly that of a baby, from the crash site for DNA testing.
"We are still searching for the fuselage. Usually, the black box wouldn't be far from the fuselage," said Air Marshal Syaugi. "We started at 10.30am… using multi-beam echo sounders. We have not picked up any sign of a large object on the sea floor."
Finding the cockpit voice recorder and flight data recorder is critical when trying to determine the cause of the crash, safety experts have said.
A team of three specialists from Singapore's Transport Safety Investigation Bureau arrived in Jakarta on Monday evening with an underwater locator beacon detector to assist with the search.
The head of KNKT, Dr Soerjanto Tjahjono, had told Reuters that underwater "pinger locators", including equipment from Singapore, were being deployed to help find the aircraft's flight recorders.
Deputy police chief Ari Dono Sukmanto said yesterday that police forensic experts are carrying out a series of tests on the remains of bodies from the crash site to establish their identities, but the process will take days.
More than 130 family members of people on board Flight JT610 have provided DNA data to the authorities to assist in the identification of victims.
Singapore President Halimah Yacob and Prime Minister Lee Hsien Loong have written to President Joko to convey their condolences, while Foreign Minister Vivian Balakrishnan has written to his Indonesian counterpart Retno Marsudi.
"On behalf of the Government of Singapore, I extend my deepest condolences to the families who lost loved ones in this tragedy," wrote PM Lee.
The three leaders also said that Singapore stands ready to offer any assistance to the search and recovery efforts.