Paul Danahar, who was travelling with UN monitors, found buildings gutted and burnt in the deserted tiny village near the western city of Hama.
It is unclear what happened to the bodies of dozens of reported victims.
Violence continued across Syria, with unconfirmed reports of explosions in the capital Damascus.
The Red Cross has warned that 1.5 million people need humanitarian aid.
Condemning the Qubair massacre earlier, UN Secretary General Ban Ki-moon warned of an imminent danger of civil war and the international peace envoy, Kofi Annan, has said his six-point peace plan is not being implemented.
The opposition blamed the Qubair massacre on militia allied to President Bashar al-Assad while the government accused "terrorists" of killing civilians.
UN monitors reached Qubair on Friday, with Paul Danahar accompanying them, after coming under fire while making an initial attempt on Thursday.
'Burnt flesh'
People in the area told the UN team that everybody in Qubair "had died except for a few", UN spokeswoman Sausan Ghosheh told BBC News after visiting the village.
She said that the UN had not yet been able to establish the number of people dead or missing and were trying to compile a list with the help of local people.
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At the scene
Paul Danahar
BBC News, Qubair
The first house had been gutted by fire. The smell of burnt flesh still hung heavy on the air.
The scene in the next house was even worse. Blood was in pools around the room.
Pieces of flesh lay among the scattered possessions.
Even butchering the people did not satisfy the blood lust of the attackers. They shot the livestock too.
The only clue as to where the bodies of the dead people had gone was etched into the tarmac of the road nearby. The tracks were made by military vehicles, said a UN observer.
Read Paul's eyewitness account in full
According to Ms Ghosheh, one house in Qubair seemed to have been hit by tank rounds as well as weapons of different calibres, including small arms.
A second house, she said, had "burnt flesh inside and... a stench of burnt flesh".
Activists say government forces removed many of the bodies from Qubair but a number are said to have been buried in the nearby village of Maarzaf.
The opposition Syrian National Council gave a death toll of 78 but another organisation, the UK-based Syrian Observatory for Human Rights, has a figure of "at least 55". State media gave a figure of nine.
The militiamen accused of the killings at Qubair are known as shabiha, and are mainly from the minority Alawite community of President Bashar al-Assad.
The Alawites are a heterodox offshoot of Shia Islam.
The victims appear to be mostly Sunni Muslims, who make up the majority of the population.
Analysts say the major fear is that Syria falls victim to the kind of sectarian violence that tore Lebanon apart for decades.
Annan plan dead?
Speaking at the UN in New York on Thursday, Mr Ban warned the danger of full-scale war was "imminent and real".
While the Annan plan remained the focus of peace efforts, he said, urgent talks were needed on how further to proceed.
Speaking in Washington on Friday, Mr Annan said: "Some say that the plan may be dead."
Both China and Russia have twice blocked Security Council resolutions against Syria and have restated their opposition to outside military intervention in the conflict.
A senior US official has expressed concern about reports that Russia could be helping Syrian institutions evade financial sanctions.
After a visit to Moscow, Treasury official David Cohen told BBC News there was evidence that financial sanctions against Syria were having an impact but Washington was worried that Russia's close economic ties with Syria were undermining the programme.
The International Committee of the Red Cross says about 1.5 million people are in need of humanitarian aid in Syria.
Its aid workers report that food, medical care and shelter are in short supply and even bread has become hard to find, while more and more people are being driven from their homes.
Blasts in Damascus
