(Adds shooting deaths, quotes, details, recasts top)

By Tom Ashby

ABUJA, April 21 (Reuters) - Troops shot dead three boys during a protest, thugs stole ballot boxes and millions of voting slips went missing in Nigeria's election on Saturday, dashing hopes of a smooth democratic transition.

The vote will seal the first handover from one civilian president to another in Africa's most populous nation, scarred by three decades of corrupt military rule.

But hopes the election would be a beacon for African democracy were lost in a catalogue of abuses and confusion.

As polling stations closed at 5 p.m. (1600 GMT) European Union observer Max van den Berg said he was unsure there would be any improvement over regional polls last week, when there was widespread fraud and 50 people were killed. "For the moment I am worried," he told Reuters, but said it was too early to come to a final conclusion.

Troops shot dead three boys aged between 11 and 17 during a protest in the northern town of Daura against alleged rigging, hospital sources said. It was not clear if the victims were protesters or bystanders. Ten other people were injured.

Hours before polling stations opened, unknown attackers tried to blow up national electoral headquarters in the capital Abuja with a fully laden petrol tanker. It hit a telephone pole outside the building and did not explode.

Opposition parties said millions of ballots went missing.

Reuters correspondent Estelle Shirbon saw national electoral commission officials in southern Bayelsa state stuffing dozens of completed votes into ballot boxes.

A young man, who gave his name as James, complained he had thumb-printed 50 ballots for the ruling People's Democratic Party (PDP) but had not been paid.

PROTESTS

Opposition leader Muhammadu Buhari said no one could claim to have won an election with so many irregularities.

"It is likely we will call our supporters as from Monday to come out and protest if the PDP announce they have won the election," he told Reuters in an interview.

"It is not a question of winning because I don't think there have been elections."

Troops opened fire in Daura, Buhari's hometown, when hundreds of youths smashed cars and set fire to roadside shacks after thousands of ballots were reported missing.

Voters in two local government areas of southeastern Anambra state had already left polling stations on Saturday evening when voting materials finally arrived. Ballots never arrived at another two polling units visited by a Reuters correspondent.

The opposition Action Congress party said: "In every state where the party has a large followership, INEC (Independent National Electoral Commision) deliberately ensured inadequate supply of voting materials."

Thugs in northern Kano armed with swords and guns stole ballot boxes, while an election official in southwestern Ondo state was abducted by a gang in police and army uniforms.

All 60 million ballots had been reprinted at the last minute after the Supreme Court ruled on Monday that the electoral commission was wrong to disqualify Vice President Atiku Abubakar, arch-rival of President Olusegun Obasanjo, as an opposition candidate.

Electoral commissioner Maurice Iwu said voting materials arrived late in a few areas, but he was pleased over all.

"On the whole we did well as a country. We should congratulate ourselves," he told a press conference.

The PDP candidate, little-known state governor, Umaru Yar'Adua, is expected to win the presidential election but the opposition says he will be Obasanjo's puppet.

The outgoing president failed to change the constitution to allow him a third term. (Additional reporting by Felix Onuah and Camillus Eboh in Abuja, Estelle Shirbon in Port Harcourt, Daniel Flynn in Katsina, Ibrahim Mshelizza in Maiduguri, Mike Oboh in Kano, Farouk Umar in Sokoto, Ijeoma Ezekwere in Onitsha, Tume Ahemba in Lagos)

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