The ministry said 12,320 civilians were killed in 2006 in what officials call "terrorist" violence - half of them since September.
The December figure is three and a half times that of January's - before the surge in sectarian killing that followed the bombing of a Shia shrine in February.
A figure of 3,700 civilian deaths in October, the latest figure published by the UN, based on data from the health ministry and the Baghdad morgue, was branded exaggerated by the Iraqi government.
The UN figure indicates about 120 civilians died each day. The government has stopped publishing its own figures and has barred its officials from giving out such data.
Parties affiliated to the government have been accused of involvement death squads and militias.
An interior ministry official said the December figure included people killed in bombings and shootings but not deaths classed as "criminal".
The tally in October was 1,289.
The interior ministry said 125 police officers and 25 Iraqi soldiers were killed in December, similar totals to November and October.
The US military says 112 American soldiers were killed in December, the deadliest month for them in two years.
Just before New Year, the total US death toll since the invasion of March 2003 passed the 3,000 mark.