The ministry of information said it has "successfully jammed the signals" of the station.
However, the BBC's Abdussalam Ahmed in Enugu says Radio Biafara is still broadcasting.
It is not clear where it is based but it mainly broadcasts to the Igbo-speaking south-east of the country.
The first republic of Biafra declared its independence from Nigeria in May 1967, but was eventually defeated after a three-year civil war that cost more than one million lives.
Our correspondent says the station hosts phone-in programmes with listeners calling to talk about issues affecting their region and their desire to break away from Nigeria.
It also attacks and ridicules President Muhammadu Buhari and other government officials.
Although the Biafra uprising was quelled by the military, a group called the Movement for the Actualisation of a Sovereign State of Biafra (Massob) has attracted the support many young people in the region.
They feel they have been discriminated against by those in power in Abuja and demand independence.
Several of their leaders and sympathisers have been detained by authorities and accused of treason.
Nigeria's government has vowed to shut down an illegal radio station operated by people sympathetic to the breakaway state of Biafra.