Outgoing Aviation Minister Stella Oduah, a close ally of the president, is the most high-profile sacking.
She has been embroiled in allegations of corruption, which she denies, after her ministry spent $1.5m (£1m) on two bullet-proof luxury cars.
Mr Jonathan's party is divided on whether he should seek re-election.
The governing People's Democratic Party (PDP) has been hit by a wave of defections to the opposition All Progressive Congress (APC), which has cost the PDP its majority in the House of Representatives.
Several state governors have also switched sides.
Last month, Mr Jonathan also sacked all his military chiefs over their inability to end the Boko Haram Islamist insurgency in the north.
As well as Ms Oduah, Mr Jonathan also sacked the minister of police affairs, the minister of the Niger Delta, home to the country's huge oil wealth and the state minister of finance.
Correspondents say it is a surprise that he has replaced Ms Oduah, as she was instrumental in raising funds for his last election campaign.
BBC Hausa's Aliyu Tanko says the recent wave of sackings shows that President Jonathan wants to be surrounded by popular people, not those tainted by scandal, in case he decides to seek re-election.
He is also trying to exert his authority to address his image as someone who is being controlled by more powerful figures, our correspondent says.
Mr Jonathan has said that he would only serve one term after his election in 2011 but there is a widespread belief that his allies are preparing for him to stand for re-election.
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