Victims' relatives and many ordinary Russians believe the authorities covered up what happened two days later, when federal troops stormed the school and a firefight with the hostage-takers left hundreds dead.
Officials say the death toll was so high because the hostage-takers set off a bomb inside the school, forcing troops to intervene.
But many survivors and independent investigators say soldiers deliberately started the battle with an incendiary rocket-propelled grenade - a highly destructive weapon that brought down part of the school's roof and started a fierce fire.
Many witnesses also say they saw tanks fire shells into the school, something that officials deny.
Over 3,000 mourners entered the school on Saturday under heavy guard, weeping, carrying candles and laying flowers in the burnt-out shell of the gymnasium where the hostages were held.
In an emotional letter, the Beslan Mothers Committee demanded that Vladimir Putin, the Russian president, apologise to the 186 children killed in the massacre.
"Come to the graveyard in the final year of your leadership and say: 'Forgive us, children, we sacrificed you for the safety of millions of other Russian children. We couldn't defeat terrorism in Russia in any other way.'"
Putin, speaking in Russia's Caspian Sea city of Astrakhan on a day that is celebrated elsewhere in Russia as the start of the school year, said: "We cannot forget about the children that will never go to school - I mean the tragic events in Beslan."
"We should remember that today," he told children at a local school.
In Beslan, portraits of the victims lined the scarred walls inside the gymnasium, as did signs reflecting the enduring emotional and political turmoil.
"There is no forgiveness for the authorities for allowing Beslan," one said.
"The federal security service and interior ministry are responsible for terror," read another.
Three years after the massacre, there is anger that virtually the only person to have been punished is the sole surviving hostage-taker.
|A monument dedicated to the |
children in St Petersburg [AP]
Susanna Dudiyeva, who lost her 13-year-old son and heads the Beslan Mothers Committee, said: "Three years after the attack, there are fewer of us, but we will still find out the truth."
Russian newspapers and independent investigators have publicised a series of blunders on the part of federal and local authorities, ranging from failing to act on intelligence to botching the rescue attempt.
Three local policemen were found guilty of negligence, but they were granted amnesty earlier this year.
Boris Gryzlov, head of the United Russia party, and regional presidential representative Dmitry Kozak laid flowers in the school and met with the Beslan Mothers Committee afterwards.
Kozak vowed that any officials found criminally negligent would face trial, while Gryzlov said that ballistic experts would hold a simulation near Moscow of the firefight by the end of the year as part of the investigation.
Timuraz Chedzhemov, the victims' lawyer, said he was dropping a case against local officials after receiving a death threat by telephone earlier this month.
"I did everything I could to establish the truth. Whoever thinks I'm a coward, let him take my place. The mothers of Beslan need help, not sympathy," he said.