He extended condolences to all families who lost members in the crash and the government and people of Ondo State who were plunged into sorrow while preparing to bury their former governor.
A statement by his Special Adviser on Media and Publicity, Dr. Reuben Abati, said: "The President feels and shares the grief and pain of the Agagu family as they grapple with the further loss of beloved relatives and associates so soon after losing their husband, father and mentor."
"He prays that God Almighty will comfort the Agagu family, as well as their relatives and friends, and grant them the divine grace they will undoubtedly require to overcome the trauma of this most trying time."
"President Jonathan views the plane crash as most unfortunate and regrettable, even with the concerted efforts of the Federal Government to enhance aviation safety in the country.
He, therefore, ordered a thorough investigation of the crash by all relevant agencies with a view to determining the cause and taking further actions, as may become necessary.
The President also summoned Aviation Minister Stella Oduah to the Presidential Villa following the crash. The call came as she prepared to brief the media on the tragic incident yesterday.
The briefing was suspended as Oduah said: "I am sorry to have come late but I will tell you that I just received a call from the Villa and I need to attend to it."
In the Minister's already prepared speech made available to reporters by her Special Assistant (Media), Joe Obi,
Mrs Oduah said the number of persons aboard the aircraft as at time of departure was 20, including the crew.
She added that the Fire Service Department, Federal Airport Authority of Nigeria (FAAN) immediately drafted a team of rescuers at the crash and were able to stop the inferno.
She said: "The control tower immediately activated the crash alarm of the airport as the first step of the emergency response procedure. The first responder immediately proceeded to the crash site.
"The FAAN fire service department, ambulances and other relevant emergency apparatus successfully extinguished the fire within 2 minutes despite the surging crowd."
Oduah said relevant authorities had started to contact families of the victims stressing that information about identities of the victims would be made available later.
She said the Black Box of the aircraft had been located and already in possession of the Accident Investigation and Prevention Bureau (AIB).
According to her, further activities which involve identification of the cause of crash would be jointly conducted by the AIB and Nigerian Civil Aviation Authority (NCAA) as she commiserated with families of the deceased.
"While it is too early to determine the cause of the accident, we urge the public to be patient while the investigation progresses. I assure the public that the investigation will be thorough and that our airspace remains safe and secure," Oduah added.