The disclosure was made by the presidential spokesman, Femi Adesina on Saturday in a state house press release.
Buhari, elected in March on promises to combat corruption, has made clear he wants to overhaul the oil sector in Africa's biggest economy, which provides the government with around 70 percent of its revenue.
He has said his government will trace and recover what he called "mind-boggling" sums of money stolen from the oil sector.
"Mr President will soon split the NNPC into two entities. One will be an independent regulator and the other one an investor vehicle," said the spokesman, who did not a provide a timeframe for the restructuring.
The NNPC currently represents national interests in oil and gas exploration, manages the energy sector and is the industry regulator in Africa's top crude producer.
It has been accused of failing to account for billions of dollars in the last few years although it has said that the money was not lost.
An NNPC source, who wished to remain unnamed, said the planned changes were long overdue.
"We can't continue to be a regulator, a revenue collector and a business, all rolled into one. That gives room for a lot of confusion, obfuscation and misrepresentation," he said.
Last month Buhari dissolved the NNPC board and more sackings are expected.
The president, who has said he will not appoint a cabinet until September, is widely expected to keep the petroleum portfolio for himself.
Under the constitution, the NNPC is supposed to hand over its oil revenue to the federal government, which then pays back what the firm needs based on a budget approved by parliament.
But the act establishing the state oil company allows it to cover costs before remitting funds to the government.
Last month, the National Economic Council said the NNPC had earned 8.1 trillion naira ($41 billion) between 2012 and the end of May 2015, but paid only 4.3 trillion naira ($21.6 billion) to the federal government.
A 2013 investigation by former central bank governor Lamido Sanusi found the state oil company had failed to pay $20 billion in revenues to government accounts between January 2012 and July 2013.
The NNPC argued that the money could be accounted for. A subsequent inspection of NNPC accounts by PwC found that some funds were unaccounted for, but bemoaned a lack of cooperation and led to the issuing of an audit with extensive caveats.