The NDC said former President John Mahama's brother did not commit any crime when he issued 44 cheques to the Ghana Revenue Authority (GRA) that turned out to be dud.
The cheques were to offset debts incurred by two companies - MBG Limited and Holman Brothers - for the clearance of some heavy duty equipment at the Tema Port in 2015.
NDC National Organiser, Kofi Adams told Alpha radio, government's handling of the issue smacks of an attempt to victimise the businessman because of his link to the past administration.
"Ghanaians did not spend time to vote for a government to go after political opponent to destroy their businesses," he said. "This is not right."
The Economic and Organised Crime Office (EOCO) has directed the Chief Executive Officer of Engineers and Planners to pay the amount of GHC12 million owed the state by May 8, 2017.
This followed several failed attempts by the GRA to redeem the money from Mr Mahama.
The former President's brother was invited by EOCO to aid it in its investigation of the matter on two occasions last week. He was invited on Tuesday and Friday.
After some interrogation which lasted for eight hours, the businessman was asked to make payment or risk losing the equipment he cleared at the Port.
GRA Assistant Commissioner for Communications, Robert Mensah told Joy News the Authority has given Mr Mahama two weeks to ensure his companies redeem their debt..
But the NDC has, from the first day the businessman was invited, described the probe by EOCO as "political witch hunting" triggered by government.
Mr Adams said it is not right for government to terminate the payment arrangement between Mr Mahama and GRA. "Why defy this arrangement and make it criminal?"
He said Mr Mahama has not denied owing the state for which reason he does not deserve the bad reportage which could potentially affect his businesses in the country.
"This government must stop witch hunting innocent citizens," he said.