Malawi, one of Africa's poorest nations, was considering selling off the financially struggling Air Malawi as part of a drive to lessen the government's financial burden in key sectors, including transport and telecommunications.
Comair, a partner of British Airways, emerged as the frontrunner to buy Air Malawi last year.
"We rejected their bid because they were interested in taking over the whole company while we were only looking for a strategic partner to help us run the company," Mussa told Reuters.
"We have decided to put the whole sale on hold until we have further consultation with other stakeholders."
Malawi's trade unions have criticised the government's privatisation campaign, arguing that previous sales of state assets have led to job losses and failed to make companies profitable.
The government, which decided to sell Air Malawi in 2000, said it is reevaluating its privatisation efforts.
Established in 1967, Air Malawi has two Boeing aircraft and one other plane. Its international routes include flights to London, Johannesburg and several other cities.