Nkunda says he is protecting his own minority ethnic Tutsi population in North and South Kivu provinces from locally based Rwandan Hutu fighters, whom he has accused the Kinshasa government of backing.
In 2004, he led two army brigades, around 4,000 men, into the bush and briefly captured Bukavu, the capital of neighbouring South Kivu.
The rebel general is wanted by the UN for alleged war crimes and is considered by them one of the most wanted regional commanders still at large in the country.
"We were in a ceasefire in January. But what is happening on the ground is that the government has put an end to that process, " he told Al Jazeera.
"We are afraid that because the government is working with negative forces in Rwanda that were responsible for the genocide there that they want to kill our people in North Kivu.
"I'm fearing that those negative forces want to do a genocide in Congo."
Chikez Diemu, the Congolese defence minister, told Al Jazeera: "Everybody knows Mr Nkunda is a criminal. Everybody knows he has killed people."
Diemu insisted that the army had not been sent to fight but carry out an agreed programme to integrate Nkunda's forces into the army.
After bouts of fierce fighting last year between the regular army and forces loyal to Nkunda, the two sides agreed to integrate the mainly Tutsi forces into special "mixed" brigades in Nord-Kivu.
Five such brigades have been deployed since January but UN monitors say this has only worsened the situation.
Colonel Philemon Kav, an army brigade commander, said Nkunda's forces sustained "heavy losses" when they launched a pre-dawn offensive on Thursday in a bid to overrun at a key post south of Masisi, the main regional town.
Nkunda denied the claim, saying: "We have not taken many casualties and morale is high."
He also warned that the conflict could spiral out of control and threaten regional security.
The UN says more than 170,000 civilians have been displaced in fighting in the region since the beginning of the year.
On Thursday, witnesses said that the populations of entire towns had fled the fighting.