At the heart of the problem lay increased diesel prices and higher operatoring costs.
Saboa said the subsidies, which was created to make up half of the ticket costs passengers pay, had to increase on average with 7,45% per year since 2009 to keep pace with cost increases, but has only inceassed on average by 1,78% per year between 2009 and 2013.
Saboa represents more than 75% of the bus services in South Africa and transport more than 1,5 million commuters each day.
Another problem is that route contracts are renewed monthly, a temporary system that has been in place for the past 17 years.
Tiyani Rikhotso, spokersperson for the departement of transport, said they were aware of the situation and that bus operators want three year contracts.
He said effecting changes to the current temporary system differed for each of the nine provinces and could not tell the committee when the process would be finalised.