Irina Gagloyeva, a spokesman for the South Ossetian defence ministry, told Russia's Itar-Tass news agency that she had no information about any withdrawal but that South Ossetian police were replacing Russian peacekeepers in Tskhinvali.
Two of Russia's state-controlled news agencies also issued conflicting reports about plans to withdraw.
Itar-Tass quoted an unidentified Russian defence ministry official as saying non-essential Russian military units were departing, but Interfax quoted an unidentified official from the same ministry as saying there had been no withdrawal.
In the Georgian town of Gori, about 30km from the breakaway region of South Ossetia, Borisov said that Russian regular forces were being replaced by Russian peacekeepers.
But tanks and armoured personnel carriers were still in place around the town and on the road south towards the Georgian capital Tbilisi.
"We are hearing from Russian military contacts around the town that the troops in Georgia are considered to be last in, so they will be the last out," Al Jazeera's Alan Fisher, reporting from inside Gori, said.
"In Gori itself there is still a very high Russian presence ... you can still see many Russian troops, they are digging trenches, their armoured personnel carriers, their tanks are now well hidden under camouflage."
The six-point peace pact, signed by Medvedev on Saturday, requires all forces in Georgia to withdraw to positions held prior to the conflict, which began on August 7 after Georgian forces began a bombardment of the breakaway region of South Ossetia.
Under the deal, Russian troops, which entered the conflict to support the South Ossetian separatists, have the right to patrol "a few kilometres" deeper inside Georgia beyond the South Ossetia conflict zone, Georgian and French officials said on Saturday.
Kakha Lomaia, secretary of the Georgian security council, told the Reuters news agency that some of the Russian force in Gori had been redeployed to Khashuri and Akhalgori, effectively widening their presence in Georgia.
Russian troops were reported to effectively control the city and air base of Senaki, which which sits on a key intersection controlling access to the Black Sea port city of Poti and the road north to Abkhazia.
Russia also confirmed on Sunday that troops had taken over a major power plant in western Georgia.
"What we see on the ground clearly shows that Russia is not abiding by the ceasefire that its president has signed ... as of today we are not seeing any reversal of this threat, we are not seeing any withdrawal at all," Shota Utiashvili, Georgia's interior ministry spokesman, told Al Jazeera
The French-drafted ceasefire agreement signed on Saturday calls for an end to all military action, free access to humanitarian aid. It also calls for a demilitarised border zone.
Sergei Lavrov, the Russian foreign minister, confirmed that Medvedev signed and ordered the implementation of the ceasefire deal, but said Russian troops would not withdraw until Moscow was satisfied that security measures it forces are allowed to take under the agreement are effective.
|Russian troops were seen heading to Tskhinvali despite ceasefire reports [AFP]
"As these additional security measures are taken, the units of the Russian armed forces that were sent into the zone of the South Ossetian conflict ... will be withdrawn," he said.
"We are constantly encountering problems from the Georgian side, and everything will depend on how effectively and quickly these problems are resolved."
Even if Russian forces do withdraw from the rest of Georgia, Moscow appears likely to maintain strong control over the provinces.
Lavrov said on Thursday that Georgia can "forget about" South Ossetia and Abkhazia, which broke away from Georgian government control during wars in the early 1990s.
Moscow, which firmly backs South Ossetia and Abkhazia, has issued Russian passports to most people in the two territories.