Abdullahi replaces Omar Suleiman, who has been relieved of his appointment, according to an Aso Rock statement on Wednesday.
Abdullahi who hails from Kano State, was Acting Executive Director (Finance & Administration) of NPA.
He holds a Bachelors degree in Political Science and Masters degree in Public Administration.
Jonathan also approved the appointment of three new Executive Directors for the NPA.
They are David Omonibeke (Marine & Operations); Mohammmed Sani Saleh (Engineering & Technical Services); and Olumide Oduntan, Finance & Administration).
Other appointments made on Wednesday by Jonathan were three new Executive Directors for the Nigerian Maritime Administration and Safety Agency (NIMASA).
They are Captain Ezekiel Bala Agaba (Maritime Safety & Shipping Development); Obi Callistus Nwabueze (Maritime Labour & Cabotage Services); and Baba Haruna Jauro (Finance & Administration).
The statement, issued by presidential spokesman, Reuben Abati, said all the appointments are with immediate effect.
The appointments came two days after Jonathan convened a retreat on maritime security at the Presidential Villa.
