Mrs Jonathan is also reportedly set to sue Skye Bank due to the restriction on the accounts.
The EFCC placed a restriction on the accounts as part of investigations into the affairs of former Special Adviser to ex-President Goodluck Jonathan on Domestic Affairs, Waripamowei Dudafa.
However, after the accounts were blocked, Mrs Jonathan, through her lawyer, announced that the money in question belonged to her.
News of the impending court case was confirmed to BBC by a source within the EFCC.
Mrs Jonathan is also reportedly set to sue Skye Bank, in which the monies were deposited, over the restriction on the accounts.
The former first lady had earlier written to EFCC Chairman, Ibrahim Magu urging him to unfreeze the accounts to enable her access the money which she claims is meant for her medical bills.