A UN military spokesman said the process of mixing Nkunda's forces with government forces in volatile North Kivu province would officially start later on Thursday.
Violence involving ethnic fighters has continued in the east of the country, perpetuating a humanitarian disaster that has killed an estimated four million people since 1998.
The Kinshasa government has issued an international warrant via Interpol for Nkunda's arrest for alleged war crimes committed by his forces during their 2004 occupation of the town of Bukavu.
Nkunda said on Thursday that he himself planned to rejoin the Congolese army only when the warrant was lifted.
Nkunda's forces launched attacks against government forces near the provincial capital Goma late last November, sparking a month of sporadic fighting that forced tens of thousands of civilians to flee.
But Rwandan-brokered talks in Kigali led to an informal agreement to mix Nkunda's fighters with army brigades in North Kivu, allowing them to stay in the area as part of the national army.
Other renegade forces from the war have been moved to different regions of the vast country after integration into the army.