Uganda had announced earlier in the week that it would be represented at the funeral "by the highest authority in the country" but had not specified exactly who that meant although Museveni as head of state and government fits the description.
Ugandan Information Minister James Nsaba Buturo would say only that Museveni had gone on Friday to the town of Yei in southern Sudan "to see the body and after paying his last respects, he returned to Uganda."
In Yei, the Ugandan leader raised eyebrows by suggesting the July 30 chopper crash in which Garang died might not have been accidental, contrary to official explanations.
"Some people say accident, it may be an accident, it may be something else," Museveni told mourners in Yei, noting that Garang had perished on his presidential helicopter and that an unspecified "external factor" might have been responsible.
The comments irked Sudanese officials and distressed diplomats and others in Sudan where there has been fierce speculation that Garang was assassinated.
Sudanese Information Minister Abdul Basit Sebdarat said late Friday that Museveni’s remarks were "extremely worrying" in light of the fact that an international team is now investigating the crash.
"Uttering statements or speculations ahead of the investigation would harm the probe and the chances of finding the facts," Sudan’s official SUNA news agency quoted Sebdarat as saying.
Anger over Garang’s death and conspiracy theories are blamed for much of the deadly violence in Khartoum and Juba that erupted after news of the fatal helicopter crash broke on August 1.
UN special envoy to Sudan Jan Pronk told reporters in Juba on Saturday ahead of Garang’s funeral that there was no reason to think the crash was anything other than an accident due to poor weather, darkness and possible pilot error