"Everything went very smoothly this morning," the spokesman said on condition of anonymity.
"The teams are now patrolling the areas and making their first contacts. They will report back to headquarters throughout the day."
'Buffer zone' entered
Under the terms of the EU peace deal, Moscow pledged to withdraw its troops from territories outside of South Ossetia and Abkhazia within 10 days of the EU observer mission being deployed.
Moscow had said on Tuesday that the EU mission should not immediately enter a Russian-controlled "buffer zone" around South Ossetia, but at least one EU observer team entered the zone on Wednesday.
The patrol passed through a Russian checkpoint near the village of Kvenatkotsa into the buffer zone after consulting Russian soldiers.
The mission, whcih is manned by unarmed officers, comes after Georgia and Russia agreed to observe an EU-brokered peace plan which paves the way for an eventual pull-out of Russian forces from Georgian territory.
War broke out between Russia and Georgia on August 7 after Georgian forces shelled South Ossetia, a province which wants to secede from Georgia and which has the backing of Moscow.
Russian forces quickly rolled into Georgia, routing Tbilisi's forces and maintaining a heavy military presence in the country.
Tbilisi has charged that Moscow has supported the secession claims by South Ossetia and Abkhazia in order to undermine Georgia’s relationship with the West.
On Tuesday Javier Solana, the EU's head of foreign policy, said that Russia was expected to adhere to the EU peace plan and evacuate its forces from Georgia by the October 10 deadline.
"I am optimistic that all the parties will comply, as we have done, to the terms of the agreement," Solana said.
"The objective of this mission is to allow Russian forces to withdraw."
In the wake of the August war, Moscow has recognised South Ossetia and Abkhazia as states independent of Georgia, drawing opprobrium from the US and the EU.