Representatives of RFA were called to a meeting with Cambodian Government officials who allege unfair coverage.
"The meeting was nothing more than a blatant attempt to discourage objective reporting on the government," John A. Estrella, the group's vice president for communications and government relations, told Radio Australia.
"The Cambodian government clearly does not understand the principles of a free press or the important role of independent media if it thinks it can intimidate RFA and dictate what we can or cannot report on," Mr Estrella said.
Phay Siphan, spokesman for the Cambodian government's Council of Ministers, told the Connect Asia program that there had been a "misunderstanding" and denied they were trying to manipulate RFA.
"We don't touch anything else, (we ask) just to watch the language, respect local qualities and local cultures," he said.
The meeting with Radio Free Asia comes ahead of national elections in 2013, which will see the entrenched Cambodian People's Party challenged by a newly-merged opposition coalition, the Cambodia National Rescue Party.
However, Mr Siphan said the issue of elections was not discussed at the talks.
RFA is one of the few sources of independent news in Cambodia's mostly politically-aligned media.
It broadcasts Khmer-language programs on Beehive Radio, along with Voice of America, while Radio Australia broadcasts in English and Khmer on 101.5FM in the major urban centres of Phnom Penh, Siem Reap and Sihanoukville.
Earlier this month, Mam Sonando, the owner of Beehive Radio was sentenced to 20 years prison for inciting rebellion.
The watchdog Amnesty International has described the charges as politically-motivated and "outrageous".