Baru was also accused of making appointments following the same pattern and trying to sabotage the successes recorded in the oil sector.
In the letter from Emmanuel Ibe Kachikwu to President Muhammadu Buhari, dated August 30 and confirmed by the oil ministry, the minister said the conduct of the head of the Nigerian National Petroleum Corporation (NNPC) lacked transparency.
The newsmen who accosted Kachikwu after he stepped out from the meeting only got a "No comment" reply when they asked him about the outcome of the meeting.
This is the first one-on-one meeting Buhari will be having with the Minister since the letter was made public.
It was however obvious that the meeting with the president was as a result of the controversy now rocking the Nigeria National Petroleum Corporation (NNPC).
Kachikwu arrived the President's office at about 11.30 am on Friday.
The minister had in a leaked memo to Buhari alleged insubordination and $25 billion (N9 trillion) scandal involving the NNPC Group Managing Director, Maikanti Baru.
He told President Buhari that the country's petroleum industry would have recorded tremendous progress but for Baru's alleged inactions.
The apparently looking journalists were said to be interested in the outcome of the meeting between the president and the minister.
Nigeria's upper chamber of parliament, the Senate, on Wednesday passed a motion to set up a committee to investigate the allegations.