KHARTOUM/JUBA (Reuters) - Sudanese queued to vote on Sunday in the first elections for almost a quarter of a century that will test the fragile unity of Africa's biggest country but which have already been marred by fraud allegations.

There were chaotic scenes at some polling centres -- south Sudan's president Salva Kiir had to wait 20 minutes under a tree for his voting station to open in the southern capital Juba and then spoiled his first ballot by putting it in the wrong box.

Queues started forming in the morning in Khartoum, where the streets were unusually quiet amid a heavy police presence. There were reports of delays, ballot paper mixups and names missing from voters' lists in other areas.

The three-day election is a key indicator of whether Sudan can fend off renewed conflict and humanitarian crisis as it heads toward a 2011 referendum that could split apart this oil-producing nation and bring independence for south Sudan.

Police said they would deploy 100,000 officers across the north to ward off unrest during the voting to choose a national president, a leader for the semi-autonomous south, assemblies and governors.

Sudan's incumbent president Omar Hassan al-Bashir, who faces an arrest warrant from the International Criminal Court for allegedly planning war crimes in the western Darfur region, seems certain to win another four-year term after the leading opposition parties pulled out of the race.

"It's not going to be a perfect election. There are no such things," former U.S. President Jimmy Carter told reporters as he joined observers from his Carter Center in Khartoum.

"But if we feel that in the elections the will of the voters has been expressed adequately then that would be the primary judgement we will make."

Opposition groups and activists have put forward myriad complaints of vote-rigging, fuelling doubts about the credibility of Sudan's first multi-party polls in 24 years.

VOTING PROCESS

In Khartoum, voters stood or sat in long lines for more than three hours to go through the complex voting process -- electors receive eight voting forms in the north and 12 in the south.

Men and women waited in separate lines and had to dip a finger in indelible green ink before voting at cardboard booths.

One of the voters in the capital's Riyadh district, El-Fatih Khidr, a 55-year-old pilot, told Reuters authorities should have opened more voting centres to cope with the crowds.

"There are a lot of crowds and there should have been more information because there is a whole new generation that have never voted," he said.

President Bashir shouted "God is great" to supporters, then took ten minutes to cast his vote at a Khartoum station where queues were dominated by voters from the army and security services.

There was a palpable sense of excitement on the streets of Juba, where many see the elections as a prelude to the referendum on southern independence. Both votes were promised under a 2005 peace deal that ended more than two decades of north-south civil war.

"This is my first time to vote and it is a good beginning that Sudan is going back to democracy. I hope it will be a foundation for future democracy," said South Sudan's president Kiir after voting.

Up to 300 women in bright clothes and other voters waited patiently for more than an hour in the southern town of Malakal as officials tried to find a vehicle to deliver voting forms, said a Reuters witness.

In Sudan's western Darfur region, the scene of a seven-year conflict between government militias and rebels, aid groups moved staff out of remote areas to cities in case of unrest.

"We're not expecting widespread violence, only things that might blow up in pockets," an aid official told Reuters, speaking on condition of anonymity.

"Everyone is prepared to hibernate if there is any trouble ... People have stocked up their houses with food and water."

In Khartoum, bus companies added vehicles as a huge number of residents poured out of the city, some of them fearing possible election reprisals and others simply happy to take advantage of the election period to visit home villages.