However, Major Paddy Ankunda, Uganda's military spokesman, said that his government had received no formal communication telling its soldiers to leave.
"We have troops in southern Sudan under an arrangement with the government there, because the threat by LRA rebels still exists," he told the Reuters news agency.
Uganda, which has had troops pursuing LRA forces in southern Sudan since 2002, said it would keep its soldiers there to stop the rebels returning to northern Uganda and threatening Ugandan security.
Machar, who has been a mediator in stalled peace talks between the LRA and the Ugandan government, said he sent a team to investigate a raid on Nyongwa village on June 14 where about 30 armed men reportedly looted food and household goods.
"The rest of the evidence is there. Indeed, it didn't turn out to be the LRA, but they were UPDF," he said.
The body of 31-year-old Jino Moga Mandara was found three days later with a head injury and stab wound, seemingly from a bayonet, three kilometres away from the scene.
Police reportedly found a military pack containing green military uniforms a pair of military boots, two ponchos, three caps and a document, as well as a small bag carrying two saucepans, two plastic plates beans and cooking oil at the scene.
While investigators say that they discovered written evidence implicating the UPDF.
Machar wrote to the chief Ugandan negotiator - internal affairs minister Ruhakana Rugunda - expressing concern about the incident.
The ceasefire team, however, did confirm that another attack on June 5 on the Congo-Sudan border, which left 27 dead, was carried out by the LRA.
Uganda's two-decade civil war uprooted two million people and destabilised parts of oil-producing south Sudan and mineral-rich eastern Democratic Republic of Congo.
The Ugandan military has forces at the border with Sudan, but it remains unclear if and how deeply they have penetrated the country.