Last year, about 150 British Army veterans of the Iraq war travelled to Uzbekistan to train with the army responsible for the killings. According to one independent witness, the British soldiers "shared tactics" with the Uzbeks.
The revelations will raise fresh questions about the UK government's support for the autocratic regime of Islam Karimov, the Uzbek president.
Craig Murray, the former British ambassador to Uzbekistan who has been critical of UK policy towards Mr Karimov, was outraged that British troops had worked so closely with Uzbek forces.
"One of the most chilling things about the massacre was that it was not a spur-of-the-moment thing," he said yesterday. "The morning after, the soldiers searched the square, methodically killing the wounded with bullets to the head.
"The idea that British Army soldiers were training alongside people who do that is simply appalling."
Last autumn, 150 officers and men of the Royal Regiment of Wales travelled to Uzbekistan to take part in a major army training operation that apparently included combat operations.
The Uzbeks codenamed the operation Timur Express, a reference to the 14th-century warlord known in the West as Tamburlaine. The exercise took place at the Farish training camp, 200 miles south-west of the capital, Tashkent.
Pictures of the operation obtained by The Scotsman appear to show British and Uzbek troops firing a machine-gun and engaging in combat simulations.
The Welsh soldiers are members of the Territorial Army and most of them had served at least one tour in Iraq,
"The soldiers were able to use their experience gained in Iraq and other operations to train the Uzbeks using British tactics," said one person who observed the Farish training operation.
Previously, the Foreign Office and the Ministry of Defence have admitted offering only support and training to selected Uzbek army officers, hoping to encourage democratic reform and Uzbekistan's participation in international peacekeeping missions.
The government has been reluctant to admit providing operational support to the Uzbek army. The last time the MoD told parliament about military support, in February 2004, ministers said Britain had provided training and advice ... focused on assisting the Uzbekistan ministry of defence with its defence reform efforts".
The United States has also faced questions about its military support for Uzbekistan, seen as a key ally in the war on terrorism. Unconfirmed reports suggest that the Uzbek army units involved in the Andizhan killings had benefited from US military training.
In a statement last night, the MoD said: "Our limited activities in Uzbekistan are designed to sow the seeds of democratic management and accountability of the military.
"The Uzbek defence minister is very forward-leaning in his desire to modernise and increase professionalism in the armed forces."
The MoD described the Welsh troops' presence in Uzbekistan as an "annual peacekeeping exercise". A spokesman was unable to say whether there would be another such exercise this year.