"In territory controlled by the M23, the media are subject to threats, censorship, control of their editorial policies, occupation and sometimes abduction of their personnel," Reporters Without Borders (RSF) said in a statement, after conducting interviews with a number of journalists in the North Kivu province.
"Journalism is threatened with extinction in this region of the Democratic Republic of Congo."
"M23 intelligence officers come to the office every evening and read all the stories. They are the ones who decide which stories we can broadcast and which ones we have to spike. You cannot refuse without risking your life," one editor told RSF.
To escape harassment from rebels, "at least 10 journalists, probably more" have fled the region, RSF said, where a number of local radio stations have had to suspend operations or shut down.
Only the UN-sponsored station Radio Okapi, based in Kinshasa, is still able to operate properly.
Journalists are also spied on by the Congolese government, who suspect them of supporting the M23, said RSF, citing the case of one local radio station manager held for the past five weeks in Goma on suspicion of spying for the M23.
The restive east of the huge country is a mineral-rich area that has been consumed by conflict for more than two decades and remains volatile.
After a precarious calm spell of several months, on Monday fighting resumed for three days between government forces and rebels.
Shelling in the flashpoint city of Goma killed three and wounded 10, and caused tens of thousands to flee, just ahead of a visit to the country on Thursday by UN Secretary General Ban Ki-moon.
"We deplore the civilian losses and destruction resulting from the resumption of hostilities," RSF said, adding that it was "particularly worried about journalists, who are being prevented from working freely".
But rebels deny threatening reporters.
Rene Abandi, head of press relations for M23, said: "This is a big lie. We are the victims of false testimony. This country's government is very good at organising smear campaigns against us."
Abandi said he could guarantee "that we want free media, that we want our critics to be able to express themselves", adding that the M23's political leader, Bertrand Bisimwa, was himself a former journalist.
Faced with the fresh unrest, Ban vowed during his visit to accelerate the deployment of UN troops to battle rebels.
Forces would be in place within "one or two months" he said Thursday.