Patience Jonathan had filed a complaint against the Economic and Financial Crimes Commission (EFCC) in September, claiming that she is the rightful owner of USD 15.6 million held in several accounts.
The accounts were frozen last July as part of a money laundering and forgery investigation of some of the president's former advisers, as well top officials at four companies.
They are suspected of laundering millions of dollars from public institutions.
The other accounts, which she claims are hers but are held by associates, are not affected by the ruling.
President Muhammadu Buhari, who was elected in 2015, has vowed to stamp out the graft that plagues the oil-rich country.
But critics have accused the ex-military ruler of orchestrating a witch-hunt against former officials of Goodluck's party.
Yesterday, Buhari was dealt a setback after one of Nigeria's leading judges was cleared of 18 corruption charges, with a judge calling the accusations "highly speculative.
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