The parallels will be "subject of further study during the investigation," Dagmawit Moges told journalists, without elaborating.
She said a preliminary report into last Sunday's Ethiopian Airlines crash that killed 157 people will be released in "30 days".
Flight 302 plummeted into farmland southeast of Addis Ababa minutes into its flight to Nairobi, killing all on board and leading to the worldwide grounding of Boeing's 737 MAX 8 aircraft.
Even before the black box data had been recovered, countries and airlines seized on the similarities between the Ethiopian and Indonesian crashes to order the Boeing model out of service worldwide.
Both planes reportedly experienced erratic steep climbs and descents as well as fluctuating airspeeds before crashing shortly after takeoff.
Questions have homed in on an automated anti-stalling system introduced on the 737 MAX 8, designed to automatically point the nose of the plane downward if it is in danger of stalling.
According to the flight data recorder, the pilots of Lion Air Flight 610 struggled to control the aircraft as the automated MCAS system repeatedly pushed the plane's nose down following takeoff.
In the case of the Ethiopian flight, the black boxes have been handed to France's BEA air safety agency, which is working with US and Ethiopian investigators to determine what brought it down