The National Broadcasting Commission said in a press release on Wednesday it was imposing sanctions on Multichoice Nigeria Limited, which owns DSTV, TelCom Satellite Ltd and also NTA-Startimes, an alliance between the state-run channel and China's Star Group.
The fines related to the BBC Africa Eye documentary "Bandit Warlords of Zamfara", which interviewed bandit leaders and victims to look at the roots of violence by armed gangs in northwest Zamfara state.
Local Trust TV was also fined five million naira ($12,000) by the commission for its documentary entitled: "Nigeria's banditry -- The Inside Story".
"Broadcasters are enjoined to be instruments of national unity and desist from falling into antics of using their platforms to promote and glamorize subversive elements and their activities," the NBC statement said.
It said the documentaries violated the broadcasting code.
The government had last week threatened to punish the BBC and Trust TV over its own documentary accusing them of "naked glorification of terrorism" and banditry.
The BBC said it stood by the report, which it said was overwhelmingly in the public interest.
Heavily-armed criminal militias, known locally as bandits, are terrorizing rural areas of Nigeria's northwest and north central states, with looting raids, abductions and attacks.
Nigeria has classified the bandit militias as terrorist groups partly to allow the military more flexibility to combat them.
Thousands of people have been killed and hundreds of thousands more displaced by the violence in recent years.
Last year, Nigeria's faced international condemnation over freedom of expression after suspending Twitter for seven months after the platform deleted a tweet from President Muhammadu Buhari's account.
Nigerian officials criticized Twitter for allowing posts from separatist agitators in the country's southeast.
Abuja lifted the suspension after demanding stricter conditions for Twitter to operate in Nigeria.