About four armed hostage-takers are believed to have escaped the storming of the school, which ended a two-day siege in the southern Russian province of North Ossetia.
"I have ordered Beslan to be sealed off, Ossetia's borders to be closed and checks to be carried out to find all people linked to the terrorist act," Putin said on Saturday.
Silent throughout the drama in which hundreds of children were held hostage in Beslan, Putin paid a three-hour visit to the shocked town.
Russian television showed Putin visiting a hospital where some of the hundreds of injured were being treated.
"One of the tasks pursued by the terrorists was to stoke ethnic hatred, blow up the whole of our North Caucasus," Putin said. "Anyone who will feels sympathetic towards such provocations will be viewed as accomplices of terrorists."
But the president himself is facing questions about the handling of the siege as well as his hard-line policy against separatists in the region, who have been linked to the hostage-takers.
By the end of the siege, at least 300 hostages, mostly children, were dead and over 700 others, including more than 300 youths, left wounded.
Most of those killed or wounded
have been schoolchildren
The families of those killed have been asking why the school building was stormed by Russian troops when hundreds of captives, mainly children, were still inside.
The European Union has asked Moscow to explain "how this tragedy could have been allowed to happen".
Other EU ministers, as well as US President George Bush and several Arab and Muslim leaders have condemned the hostage-taking and loss of life.
Although negotiations were under way, the siege came to a chaotic, bloody end on Friday when an explosion apparently caused scores of hostages to flee the besieged school amid gunfire and further blasts.
Troops then stormed the building and as a gun battle ensued, hundreds more hostages escaped.
At least 20 of the masked men and women who seized the school on Wednesday have reportedly been killed. Their identities remain unclear but the Russian authorities have linked them to Chechen separatists and said 10 of the dead were Arabs.
Separatists in neighbouring Chechnya have been fighting for independence from Russia for more than a decade.
Moscow has been widely criticised for its harsh tactics in a conflict that has left thousands of civilians dead.