The light aircraft went down shortly after take-off from Malta International Airport at around 7.20am local time (6.20am GMT) this morning.
The flight was heading for the city of Misrata, Libya and there was no confirmation of the nationality of the victims.
A witness told the Times of Malta the propeller plane suddenly tipped to its right side and "went straight down to the ground".
There were not believed to be any survivors from the disaster.
A spokesperson for the agency said it had not deployed the aircraft itself but could not immediately confirm whether staff were on board.
All departures and arrivals at Malta International Airport were stopped as recovery work continued, with flights diverted to airports on the Italian island of Sicily. Live information can be found here.