The ID card scheme has always generated controversy
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Protests have marred celebrations held to mark the start of the distribution of national identity cards in Nigeria.
Workers at Nigeria's directorate of national civic registration say they have not been paid for eight months.
Internal Affairs Minister Dr Iyorchia Ayu says the government had acquired funding to resolve the crisis soon.
ID cards were first planned more than 25 years ago by the then military ruler, General Olusegun Obasanjo. The scheme finally launched on Monday.
One of the frustrated workers told the BBC's Network Africa programme that they were dismayed that the government was hailing the success of the ID card scheme while they were suffering.
"We have only been paid in stipends since 2002 and now we are living from hand to mouth," he said.
Planning data
The BBC's Jamilah Tangaza in Abuja says the ID card scheme has been so controversial among Nigerians that previous governments had been unable to see the project through.
President Obasanjo says the ID card scheme is vital to help identify illegal immigrants and provide data for government planning.
Nigeria is Africa's most populous country, with an estimated 120 million inhabitants, including many immigrants attracted by the country's oil industry.
Some northern politicians oppose the scheme, fearing it will be used to cross-check other population records, including the voters roll.
Correspondents say that population figures are often inflated in order to increase access to government resources.