Russia is adamant that the sole reason it sent hundreds of tanks and thousands of troops pouring into the secessionist territory of South Ossetia last week, and then into the undisputed territory of Georgia, was to prevent “ethnic cleansing” and a humanitarian catastrophe.

Moscow accused the Georgian armed forces of causing 2,000 deaths among civilians, and forcing up to 30,000 refugees to flee to Russia, in what Sergei Lavrov, the foreign minister, described on Wednesday as “genocide” in the Financial Times.

The “deliberate extermination of a race” is not what is happening or has happened in Georgia, but the concept of ethnic cleansing is vital to Russia’s case to justify its “humanitarian intervention”, putting it on a par with the Nato operation in Kosovo in 1999.

There is no doubt that thousands of refugees fled to Russia from the artillery exchanges and military raids launched by Georgia against the secessionist forces of South Ossetia, and hundreds may have been killed, although independent evidence of the death toll has yet to emerge.

Now Georgia is claiming “ethnic cleansing” is taking place in reverse, with South Ossetian militia attacking ethnic Georgian villages and driving out their inhabitants.

“This is a humanitarian catastrophe unfolding in the eyes of the world, and it is not very far away,” Mikheil Sakhashvili, Georgia’s president, said on Wednesday. “It is in Europe.” He appealed for a huge humanitarian effort from the US and European Union to help cope with the refugee crisis.

According to the UN High Commissioner for Refugees, an estimated 100,000 people have fled their homes in both directions from the fighting. In the past 24 hours, the agency has increased its estimate of the internally displaced people inside South Ossetia from 12,000 to between 30,000 and 40,000. That means most of the 75,000 population is displaced, including the 25,000 still in Russia.

The UNHCR does not use inflammatory language such as “ethnic cleansing”, but it is clear that in the ethnic patchwork that is South Ossetia, with ethnic Ossetian and Georgian villages interspersed, something of that sort is happening in both directions. Fear of the Georgians drove the Ossetians north, and now Ossetian militias are reported to be driving Georgians south.

The first independent report from the ground was published on Wednesday by the non-governmental group Human Rights Watch. It said its researchers “saw ethnic Georgian villages still burning from fires set by South Ossetian militias, and witnessed looting by the militias”. They also reported on first-hand accounts of ethnic Ossetian villagers who fled Georgian soldiers during the first days of the conflict.

Speaking privately, senior Russian officials admit it will be impossible to enforce an immediate peace, in spite of the ceasefire, because of the volatile ethnic relations in the region. It is not merely in South Ossetia. The UNHCR reported that it was helping with the evacuation of 1,000 ethnic Georgian villagers in Abkhazia on Wednesday, from a settlement north of Zugdidi.

“These people are fleeing out of fear,” the UNHCR said. “There are Russian checkpoints on the roads. Fear is making people move.”

The conflict is presented internationally as a clash between Russia and the west, as represented by the passionately pro-western Georgians. That is perfectly correct. Both sides see it in such post-cold war, ideological terms. But civilians are in the front line of the victims on both sides.

“Relations between Russia and Georgia have reached a poisonous new low. But it is relations within the conflict regions that will suffer most,” said Magdalena Frichova, project director of the International Crisis Group, in a commentary for the BBC website. “South Ossetia has been ripped apart in the latest fighting.”

Both sides are trading accusations of mass atrocities. She calls for “credible and impartial investigations of violations and, if appropriate, the prosecution of perpetrators, [to] advance long-term reconciliation”.

Rachel Clogg of Conciliation Resources, a non-governmental group dedicated to conflict resolution in the region, backs that call, and says “the disproportionate use of force” by both Russia and Georgia should be acknowledged by the rest of the world.

In global terms, the casualties and the wave of refugees is small. But in Georgia – population 4.6m – it is huge, and the consequences will be devastating.