Finance Minister Ngozi Okonjo-Iweala said Transparency International failed to take into account efforts to fight corruption.
Nicknamed Nigeria’s “Corruption Cop” by local media, she said ending corruption takes time.
Out of the 146 countries, only Haiti and Bangladesh were rated more corrupt.
Ms Okonjo-Iweala said the Berlin-based organisation’s methodology was too backward looking and was “not particularly helpful”.
“If you’re doing reforms it’s important that the new moves being made are recognised,” she told the BBC’s Network Africa programme.