When contacted, NHA spokesman Kashif Zaman said the authority issued cheques of Rs 5 billion on June 29 to the firms against the sanction by the government.
He said cheques worth Rs 1.5 billion were cleared on the same day and "the remaining cheques that were deposited the next day could not be cleared".
Zaman said the matter had been taken up with the government and would be resolved soon. Asked about suspension of work by the contractors, he said that the progress on the projects "had not been affected" and most of the projects in question would be completed by December.
The CPEC will connect China's Xinjiang region with Pakistan's Gwadar port giving it access to the Arabian Sea.
While India opposes CPEC's route as it cuts through the disputed part of Kashmir held by Islamabad, experts feel Pakistan is already facing a massive debt burden because of the project.