Thomson Reuters
In separate statements posted on the company's website, Mitsubishi Aircraft Corporation attributed both aborted flights to issues with the plane's air conditioning or "air management" system.
It is unclear the exact nature of the system failure.
According to the Japan Times, the first attempted flight lasted just one hour before the aircraft returning to the company's home base in Nagoya.
"We will decide the date to resume the ferry flight based on the results of inspection," Mitsubishi wrote in a statement following the second failed flight.
The MRJ made its first flight last November after three years of delays.
With the capacity to hold 80 to 90 passengers, the MRJ will enter an increasing crowed regional jet market when it enters service in 2018. The MRJ is expected to join China's ARJ21 and Russia's Sukhoi Superjet in a market currently dominated by Bombardier and Embraer.
According to the Mitsubishi, the MRJ's new Pratt & Whitney engines and advanced aerodynamics return 20% better fuel economy than regional jet currently on the market.
Mitsubishi currently has more 220 orders for its regional jet.