BAGHDAD (Reuters) -- Gunmen looted polling stations in Iraq's restive Niniveh province during the January 30 election, tampering with ballot boxes and preventing thousands from taking part, the country's Electoral Commission says.

Niniveh's capital Mosul, 390 km (240 miles) north of Baghdad, is one of the hottest spots in a raging insurgency against U.S.-led troops and has seen numerous guerrilla attacks since November.

Electoral Commissioner Safwat Rashid told a news conference on Monday that only 93 of a planned 330 polling centres managed to open for the historic vote in the province and a subsequent probe had found numerous cases of intimidation.

"There were a number of polling stations where voting materials were looted by gunmen ... The Commission regrets that a number of people were not able to cast their votes," he said.

As a result, the Commission has set aside 40 out of a total of 455 ballot boxes and these are now being examined in Baghdad for signs of fraud or tampering.

Iraqi election monitors estimate that well over 20,000 residents around Mosul were denied a chance to vote. About 100 mainly Christian protesters marched in Baghdad on Sunday to demonstrate against election irregularities.

Millions of Iraqis defied militants to take part in the election last week but the results remain unclear with only a partial count available from 13 of the country's 18 provinces.

This places a Shi'ite Islamist coalition in first place with 2.3 million votes, the Kurds in second on 1.1 million and a bloc led by interim Prime Minister Iyad Allawi on around 620,000.

Rashid was unable to say when the counting will be over, although the Commission has previously said that it hoped to get the job done by Thursday.

But he denied that evidence of intimidation and the delay in delivering the result could sap public confidence in the ballot's fairness.

"I think legitimacy has something to do with the final number of votes at the end of the counting. Then we can talk about legitimacy," he said.