Others affected were Environment Minister Hadiza Ibrahim Mailafa, National Planning Minister Shamsudden Usman, Education Minister Ruqayyatu Rufa'I, Science and Technology Minister Ita Okon Bassey Ewa and Housing Minister Ama Pepple.
Junior ministers sacked are Agriculture Minister Bukar Tijani Borno, Defence Minister Olusola Obada and Power Minister Zainab Kuchi.
Jonathan made the announcement after the weekly Federal Executive Council (FEC) meeting held with all ministers and presided over by him.
The president had introduced a Performance Contract Agreement (PCA) with the ministers last August but said the ministers would not be removed based on the assessment.
Nigeria is Africa's largest oil producer and has a population of over 150 million.
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