The service was a part of the celebrations of the 1,020th anniversary of the conversion of Kievan Rus to Christianity by Vladimir.
Ukrainian law enforcement officers told RIA-Novosti on Sunday that the believers were cordoned off to avoid a stampede, but the news agency reported that there appeared to have been enough free space near the monument.
The celebration again stressed growing tensions with Ukraine, which declared a pro-Western course after the 2004 Orange Revolution.
Ukrainian President Viktor Yushchenko, who has called for the establishment of an independent Ukrainian Orthodox Church, did not come to meet Alexy as he arrived at Borispol Airport on Saturday.
Yushchenko appealed on Saturday to the leader of the world's Orthodox believers, Patriarch Bartholomew of Constantinople (now Istanbul), to allow the creation of a Ukrainian church, a move Bartholomew suggested that he was ready to consider.
On Sunday, Alexy warned that the move was an attempt to drive a wedge between the Orthodox believers in Russia and Ukraine.
"By raising doubts about what has been undisputable for centuries, we endanger our common future," he said, Interfax reported.
He added that the "unity of Russian Orthodox Christianity does not interfere with the full-fledged lives of sovereign states that are heirs of Kievan Rus."
An independent Orthodox church was formed in Ukraine after the 1991 collapse of Soviet rule, but it remains unrecognized by any other Orthodox church. The Ukrainian branch within the Russian Orthodox Church remains its sole representative.
On Sunday, Alexy said the Russian Orthodox Church "had created all conditions" necessary for its Ukrainian branch to minister to local believers.
The tension surrounding church divisions has unfolded against the backdrop of disputes between Moscow and Kiev over gas prices, Ukraine's drive to join NATO and steps to remove Russia's Black Sea Fleet from Crimea by 2017.
Yushchenko has long called a single, independent and fully recognized Ukrainian Orthodox Church vital to forming the country's national identity.
"I believe any sort of division among Ukrainian believers will be short-lived. I believe we will achieve our dream," Yushchenko told tens of thousands of clerics, parishioners and officials in the rain outside Kiev's 11th-century St. Sofia Cathedral on Saturday.
In his remarks, Bartholomew referred to the historical difficulties of Orthodoxy in Ukraine, including the "annexation" of both the Ukrainian Church and state by Russia under Peter the Great in the late 17th century.
On Sunday, Russian television showed dozens of people shouting "Alexy is our patriarch" in Kiev.
Alexy only agreed to attend after securing an agreement that the independent, Kiev-based church would not take part in the ceremonies.
MT, Reuters
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