The transport ministry sent three inspectors to Kumamoto on Friday after a malfunctioning engine on a Japan Airlines plane ejected parts that damaged property below.
The problem occurred shortly after the Tokyo-bound plane took off from Kumamoto Airport on Thursday, forcing it to return for an emergency landing.
The government has classified the case as a "serious incident."
A turbine blade in the rear of the left engine sustained widespread damage, but it is unlikely to have been caused by a bird strike, according to the Land, Infrastructure, Transport and Tourism Ministry.
"I instructed JAL not to wait for the ministry's investigation but to go ahead with investigating the cause and take the necessary countermeasures," said Keiichi Ishii, the transport minister, at a news conference Friday.
The parts cracked the window of a clinic in Mashiki and also damaged a car on the premises, but no injuries were reported, local police said.
At least 10 parts, all about 5 centimeters long, were found within a few dozen meters of the clinic.
JAL officials visited the clinic's director, Masaaki Yamamoto, on Friday to offer an apology and a promise of compensation.
"I am horrified at the thought of the engine parts hitting my grandchildren," said 70-year-old Masao Haraguchi, who lives near the clinic with his two grandchildren. Haraguchi said he found a 5-cm piece of metal on his property after taking a walk at 5 a.m.
The Boeing 767-300 carrying 209 passengers and eight crew members returned to the airport at around 3:55 p.m., after abnormal vibrations and a rise in exhaust gas temperature in the left engine were detected roughly three minutes after takeoff, according to JAL.