The United Nations High Commission for Refugees (UNHRC) began documenting personal details of the displaced at the Dalori camp, just outside the Borno state capital, Maiduguri.
Dangana Ibrahim, from the agency, told AFP: "We are capturing their data and issuing them with temporary ID pending the production of the ID card in the next week."
At least 20,000 people have been killed and more than 2.6 million displaced in the eight-year conflict, which has destroyed livelihoods and triggered a humanitarian crisis.
According to the UNHCR, 99 percent of vulnerable IDP (internally displaced people) households in Borno state lack legal documentation.
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Even before the insurgency began, levels of registration and documentation were low, and were compounded by lack of literacy. When fighting broke out, civilians were at risk.
Ibrahim said a female IDP had been shot as a soldier mistook her for a suicide bomber, as she could not produce any identification.
In May, UNHCR regional representative for West Africa, Liz Ahua, said more than 200,000 Nigerian refugees in Niger, Chad and Cameroon also lacked "adequate documentation".
"The link between issues of statelessness, sustaining peace and security in the region cannot be separated as statelessness can lead to insecurity and instability.
"Stateless persons could easily be used as tools of destruction."
Borno state is being given priority for ID cards because it has been hardest hit by the insurgency but Ibrahim said there were plans to extend the scheme.
The UNHCR is working with Nigeria's National Identity Card Management Commission, as well as village chiefs of displaced communities, he added.
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