The deal requires Russian forces to withdraw to positions held before the conflict, but troops were still outside the strategically important town of Gori, 60km northwest of the capital Tbilisi on Saturday afternoon.
Two tanks and four armoured personnel carriers remained at Igoeti on the main road from South Ossetia to Tbilisi, just 30km away.
Andrei Nesterenko, Russian foreign ministry spokesman, told Al Jazeera that Russian forces were carrying out an operation "focused on neutralising the danger which is coming from the huge depots of ammunition and military equipment which have been left by the Georgian army".Withdrawal halted
Al Jazeera's Alan Fisher, reporting from the outskirts of Gori, said that the agreed Russian withdrawal from Gori had halted at Kaspi junction.
"They are taking up defensive positions 2km north of Kaspi junction, and there is word of talks between Georgian and Russian troops," he said.
"It appears the Russians are not going anywhere, at least not until they are ready."
Shota Utiashvili, Georgia's interior ministry spokesman, said that troops had destroyed a railway bridge in Kaspi, "paralysing the Georgian railway network".
However, Colonel-General Anatoly Nogovitsyn, deputy chief of Russia's General Staff, said: "We are now in peacetime. Why should we be blowing up bridges when our job is to restore?
"This therefore can only be yet another completely unverified statement. We are not conducting bombardments. I can say with full responsibility that this cannot be the case."
Television showed one end of the bridge collapsed against the river bank. Villagers told the Reuters news agency that explosives were detonated remotely by men in military uniforms.
Russia had said it would sign the ceasefire pact only if it saw the Georgian president's signature on the document. Russia's foreign ministry was quoted by the Interfax news agency as saying that demand was met on Saturday.
|Saakashvili, right, held five hours of talks with Rice [AFP]
Al Jazeera's Neave Barker, reporting from Moscow, said that the ceasefire pact was being hailed as a success for Russia.
"The original six-point plan had a different sixth point ... it only said that the status of Abhazia and South Ossetia would be up for negotiation in talks by the international community," he said.
"What the Russians did on Tuesday was add an extra dimension to that, they said that they want to have international peacekeepers in the two breakaway regions, Russian peacekeepers as well as the removal of Georgian forces from both zones.
"Quite clearly, what Saakashvili has agreed to is a reduction in any influence, on the Georgian side, in these two areas."
Saakashvili signed the pact following five hours of talks with Condoleezza Rice, the US secretary of state, on Friday.
Next week Rice will travel to Brussels where she will meet Nato foreign ministers and EU officials in an effort to shore up support for Georgia.
"The world has watched with alarm as Russia invaded a sovereign neighbouring state and threatened a democratic government elected by its people," George Bush, the US president, said in his weekly radio address, which was recorded before the deal was signed.
"This act is completely unacceptable to the free nations of the world," he said.
Angela Merkel, the German chancellor, had earlier secured the agreement of Medvedev to the EU-brokered deal but was told Moscow would guarantee the will of the people in the pro-Russian separatist regions.
Russian troops entered Georgia following Tbsili's August 7 offensive to retake South Ossetia, which achieved de facto independence from Georgia in the 1990s during the breakup of the Soviet Union.
Moscow, which firmly backs South Ossetia and Abkhazia, has issued Russian passports to most people in the two territories.