Newspapers and the opposition Democratic Left (DS) party have denounced the removal of the programmes hosted by the journalists Michele Santoro and Enzo Biagi as a political move, influenced by Prime Minister Silvio Berlusconi.
Mr Berlusconi is known to be hostile to the two RAI journalists, and in April accused them of the "criminal misuse" of public funds to push their own political agendas.
The head of the Italian journalists' union, Paolo Serventi Longhi, said the move set a dangerous precedent for Italian journalism.
"There is the legitimate suspicion that for a personal reason, or because of his private and political interests, the head of the government directed the directors of RAI to throw out Biagi and Santoro," he said.
Fabrizio Del Noce, the news director of RAI's main channel, said the shows were dropped from the autumn schedule only because they fared poorly in ratings, according to Italian news reports.
Mr Berlusconi has also denied that the moves against the journalists Mr Santaro and Mr Biagi had any political significance.
"I've never made lists and I don't have anything personal against them," he said.
"The polemics mounted because of disinformation and ill-will from the opposition."
Control
Mr Berlusconi, believed to be Italy's richest man, controls the nation's largest private broadcaster, Mediaset, which operates three national TV channels.
State broadcaster RAI, which has three public TV channels, is now governed by a more right-wing governing board, seen as sympathetic to Berlusconi.
Critics of the prime minister say this gives him effective control of 90% of the Italian TV market.
Mr Berlusconi has now acknowledged the potential for a conflict of interest, and his governing coalition has tabled legislation to set up two antitrust bodies, monitoring potential conflicts among public officials.
But the opposition has called the proposed legislation toothless.
Piero Fassino, head of the DS party, has described Mr Berlusconi's media proposals as "a new confirmation of the arrogance of the majority".