Herat is cut off from the rest of the planet. This was once one of the great cities of the world, an imperial capital drawing its wealth from trade along the Silk Road with Iran, the rest of Afghanistan and central Asia. Above the 800-year-old mosque in the city centre are minarets covered in blue and green mosaics which soar above one of the most magnificent monuments of the Islamic world.

But today Herat is cut off even from the rest of Afghanistan. I flew there because it was too dangerous to come by road. We turned right out of the battered-looking airport because, had we turned left down the main road towards Kandahar, we would soon have been in Taliban-controlled territory. The road going east to Bamyan and Kabul is risky for the same reasons.

Herat itself is peaceful compared to the rest of Afghanistan. There are police in their dark grey uniforms and forage hats checking cars, but they are relaxed and don't look as if they are expecting trouble. There are more new buildings than in Kabul, but on many construction sites work seems to have stopped.

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I met Obaidullah Sidiqi, a local businessman, at a picnic lunch in a well-watered orchard, full of mulberry and apple trees and honeysuckle, which he owns not far from the airport road. An attractive aspect of Afghanistan never mentioned in war reporting is the Afghan love of flowers. Even in front-line positions soldiers dig small trenches, fill them with water and plant geraniums.

Mr Sidiqi, after 16 years in construction, part of it for the Save the Children Fund and partly on his own account, explained that business in Herat faces unique difficulties. For instance, last year he had contracts under way which he could only visit in disguise. One was for the construction of a school in Shindand district in the south of Herat province, a Pashtun area where the Taliban are strong. Mr Sidiqi, like most people in Herat, is a Tajik. Overall, the Taliban rebellion is confined to the Pashtun, the community to which 42 per cent of Afghans belong, while in the past the Tajiks, who make up 27 per cent of the population, have been the core of the anti-Taliban opposition.

"I wanted to see how work was going at the school, but I did not dare go as myself," Mr Sidiqi told me. "So I grew my beard longer and pretended to be one of my drivers." He also had to go disguised to visit a road his company is building in Badghis province to the north-east of Herat, again in an area where the Taliban are strong. In fact, not all the danger comes from the Taliban – though it is always blamed on them – as there are plenty of bandit gangs in the mountains.

Overall, Mr Sidiqi said this year was better than last, though he did not sound completely confident that it was going to stay that way. He said that 200 local factories had shut, and Iran, where so many Afghans used to go to work, was issuing very few visas. Within Afghanistan there was pervasive corruption with the award of a contract usually determined by the size of the bribe offered to the officials in charge.

I was sympathetic to Mr Sidiqi's difficulties in moving around the country except by plane, because I faced the same problem. I had gone to Herat because last Monday US aircraft had attacked several villages in the Bala Baluk district of Farah province, which is immediately to the south of Herat. The local governor and surviving villagers said that more than 120 civilians had been killed. The US military denied that anything like that number had died and, if they had, it was the Taliban who had done it by hurling grenades into houses.

The problem was that Bala Baluk is in a Pashtun area where the Taliban are reputed to be strong. Back in Kabul Pashtuns told me that it was unfair to equate them with the Taliban, but in reality there are few Taliban who are not Pashtun. It was too dangerous to go directly to Bala Baluk, so the next best thing was to find a survivor or an eyewitness. I thought that some of the worst injured might be in Herat hospital, as the best in the area. But there turned out to be only 14 wounded and these were in Farah hospital. This could have meant that there were fewer dead than the Afghans were saying, or that the bombardment was so intense that all had been killed.

I did not meet survivors but I did talk to a reliable witness, a radio reporter called Farooq Faizy, who had gone to Bala Baluk soon after the attack happened. He said that police and soldiers nearby were frightened of the Taliban and told him it was too dangerous to go on, but he spoke to some village elders, telling them: "Talk to us and we will tell the world." He says he was none too sure who was in control of the three villages – Gerani, Gangabad and Khoujaha – that had been hit and he was careful about what he said. But he did take some 70 or 80 photographs and they bore out the villagers' story: there were craters everywhere; the villages had been plastered with bombs; bodies had been torn to shreds by the blasts; there were mass graves; there were no signs of damage from bullets, rockets or grenades.

I suspected that the US military's claim that the Taliban had run through the village hurling grenades, supposedly because they had not been paid their cut of profits from the opium poppy crop, was just a delaying tactic. Usually the US military delays admission of guilt until a story has gone cold and the media is no longer interested. "First say 'no story'," runs an old PR adage, "and then say 'old story'." By the end of the week the US was admitting that the grenade-throwing Taliban story was "thinly sourced".

Another thesis was that fighting had taken place 500 metres from the villages, and the Taliban had retreated through them, leading to the airstrikes. Farooq Faizy said he had seen signs of fighting in the shape of two burned-out Afghan army or police vehicles and a destroyed US Humvee, but they were seven or eight kilometres away from the site of the bombing. He had taken photographs of them showing the destroyed Afghan vehicles – Ford pick-ups with a machine gun mount over the bonnet. It seemed likely that this was the fight that had led to the Afghan army and their US advisers asking for air support. What the Americans never explain in Afghanistan or Iraq is why they are using weapons designed for world war three against villages that have not left the Middle Ages – which makes heavy civilian casualties inevitable.

Back in Herat, Mr Sidiqi was none too sympathetic about what had happened to the people of Bala Baluk. Like many Afghans, he felt that it was the weakness of the government, not the strength of the Taliban, which was the problem. Furthermore he felt, and this is surely true, that "neither Pakistan nor Iran wants a strong Afghanistan".