Those affected are the minister of Agriculture and Rural Development Mohammed Sabo Nanono and his counterpart from the Ministry of Power, Sale Mamman.
It’s not clear why they have been removed but a statement from the presidency says Mr Buhari took the decision after an “independent and critical self-review” of government programmes and policies.
It adds that such reviews help the administration “identify and strengthen weak areas, close gaps, build cohesion and synergy” in governance and in managing the economy.
Boosting agriculture and the economy have been among Mr Buhari’s priorities.
The current environment minister has been asked to oversee the agriculture ministry while the minister of works and housing is to take charge of the power ministry until new minsters are appointed.
President Buhari, who came to office in 2015, rarely reshuffles his cabinet.
But his spokesperson Garba Shehu told the BBC more ministers are likely to be replaced soon.