US sought assurances that intelligence was being used 'in compliance with the law of armed conflict' during long-running Ugandan battle against Joseph Kony's rebel movement

The US told Uganda to let it know when the army was going to commit war crimes using American intelligence – but did not try to dissuade it from doing so, the US embassy cables suggest.

America was supporting the Ugandan government in its fight against rebel movement the Lord's Resistance Army (LRA), providing information and $4.4m (£2.8m) worth of military hardware a year.

But a year ago officials became concerned that the Ugandans were guilty of war crimes in the long-running battle against Joseph Kony's rebel movement, which is famed for its brutal atrocities and abduction of children.

Jerry Lanier, the US ambassador to Kampala, reported on 16 December to Washington that the country's defence minister, Crispus Kiyonga, had verbally assured him that American intelligence was being used "in compliance with Ugandan law and the law of armed conflict. This pledge includes the principles of proportionality, distinction and humane treatment of captured combatants."

But Lanier continued: "Uganda understands the need to consult with the US in advance if the [Ugandan army] intends to use US-supplied intelligence to engage in operations not government [sic] by the law of armed conflict. Uganda understands and acknowledges that misuse of this intelligence could cause the US to end this intelligence sharing relationship."

Nowhere, though, does it appear that the ambassador directly told the Ugandans to observe the rules of war.

The following day the embassy reported that a captured colonel, Peter Oloya, held in prison in Gulu, had been shot on the orders of Colonel Charles Otema, the head of military intelligence in northern Uganda who was virtually running the war. Otema is reported to have been in daily contact with Uganda's president, Yoweri Museveni.

During the past two years the Ugandan army has deployed 4,000 troops in Operation Lightning Thunder to chase the LRA out of Uganda into the Democratic Republic of the Congo, South Sudan and now into the Central African Republic where, 800 miles from its original area of operation, the rebel group is thought to have fewer than 300 followers. Several of the LRA's senior commanders have been killed or captured but Kony is believed to remain alive.

Despite US support for Museveni, the US ambassador reported widespread disillusionment with the Ugandan leader's 24-year rule. In October last year, Lanier wrote: "The president's autocratic tendencies, as well as Uganda's pervasive corruption, sharpening ethnic divisions and explosive population growth, have eroding [sic] Uganda's status as an African success story.

"Holding a credible and peaceful election in February 2011 could restore Uganda's image which failing in that task could lead to domestic political violence and regional instability."