There have been media reports that Mr Mahama gave out 44 cheques over outstanding import tariffs but the cheques could not be honoured.
The Economic and Organised Crime Office (EOCO) has ordered Mr Ibrahim Mahama, to pay GH¢12.7m to the state by May 8, 2017.
The amount represents duty for construction equipment he cleared at the Tema Port in the name of his two companies MBG Ltd and Holdman brothers.
He was picked up by the anti-corruption agency last week Tuesday in relation to an ongoing investigation over the cheques.
But an Aide to Mr Mahama, Rafik insist MBG Ltd and Holdman brothers never issued 44 cheques to the GRA.
He claims 24 cheques were issued, 12 for MBG Lyd and 12 for Holdman brothers which were presented to the bank in January this year by GRA.
Rafik, added that technically the issue has been resolved pending payment before May 8.
Government, he said, is also committed to paying their liability to the company.