Jonathan is intervening in one of the country's most powerful institutions and the source of 80 per cent of government revenues.
Joseph Thlama Dawha replaces Andrew Yakubu as NNPC group managing director. Reuben Abati, a spokesman for Goodluck Jonathan's office, declined to give further details.
A senior presidency source, who declined to be named, said it was because Jonathan was unimpressed with Yakubu's handling of a parliamentary inquiry on oil corruption that was conducted in February.
(READ MORE: Nigeria's institutional fight against dirty oil)
Yakubu was not immediately available for comment. Numerous reports and audits have accused NNPC of corruption and in February then central bank governor Lamido Sanusi submitted evidence to parliament that the company had failed to remit some 20 billion US dollars it owed.
The NNPC denied the charges, but the evidence it gave to explain away the missing money was derided by critics.
(READ MORE: Nigeria's NNPC hasn't accounted for $50 bln in oil sales- cbank)
Jonathan has come under intense pressure to clean up Africa's biggest energy sector after a public outcry over corruption and waste of the country's vast energy wealth.
(READ MORE: Has oil-focused Nigeria forgone a diversified economy?)
There was similar pressure at the time of the previous NNPC management change in June 2012.
Appointments to powerful positions in a Nigerian election cycle - presidential polls are six months away - are also often linked to shoring up patronage networks.
Dawha is a Christian from Biu, an area in the largely Muslim north eastern Borno state which is currently being ravaged by an Islamist Boko Haram insurgency that has heavily targeted Christians.
(READ MORE: West Africa leaders vow to wage "total war" on Boko Haram)
He previously held another executive role within the company. Anthony Muoneke, a career lawyer, will take up management of the firm's development arm, the NPDC. Aisha Mata Abdurrahman is the new group executive director of commercial and investment and Attahir Yusuf is the new group executive director of business development.
Oil industry sources say regardless of who runs NNPC, major decisions are made by Oil Minister Diezani Alison-Madueke.
In addition to suspected corruption, Nigeria's oil sector suffers from oil theft in the creeks of the Niger Delta where tens of thousands of barrels are siphoned off each day.