The show focused on two outlets – Citizen News and Hong Kong Free Press – and whether they could finance their operations with reader subscription fees amid the economic downturn.
The production team, which finished working on the episode last month, said management informed them on Thursday that the programme would not be aired.
They said bosses were concerned that the documentary might help the two outlets raise money.
The government station has axed a number of its shows in recent weeks, citing “inaccuracies” and “bias”, with new Director of Broadcasting Patrick Li implementing a new review system for shows.
RTHK programmes are financed by the taxpayer, although management have suggested that staff could be asked to reimburse the cost of shows that never make it to air.