The army is struggling to win a 17-year civil war in the north
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President Yoweri Museveni has sent scores of senior army officers on forced leave.
Some are facing investigations and possible court martial, say reports.
A probe has concluded into the paying of non-existent soldiers, but the army has also been criticised for failing to halt rebel attacks in the north.
Brigadier Joshua Masaba, the newly appointed chief of staff, reportedly held emergency talks with the president and defence minister on Monday.
The Ugandan Monitor newspaper says the moves also appear to be a purge of those loyal to former army commander, James Kazini - who was sacked in June this year.
He was accused in a report of plundering the Democratic Republic of the Congo's mineral resources, while the Ugandan army was involved in the five-year Congolese war.
He is now at army training college in Nigeria.
The shake-up also comes just days after Lieutenant-General Salim Saleh, President Museveni's brother, resigned as one of the military's 10 MPs.
Ghost soldiers
Army spokesman Major Shaban Bantariza told AFP news agency by telephone that 28 senior officers, including Chief of Staff Brigadier Nakibus Lakara, had been sent on leave.
"Some will go to the court martial to give evidence on some allegations, while others will face a committee probing the ghost soldiers in the army's pay roll," he said
He said more details would be announced later on Tuesday.
Three of the five division commanders have been sacked, reports the Monitor newspaper, as well as the director of military intelligence.
Brigadier Lakara confirmed that he had been sent on leave but said he had not been told why.
"Maybe I will be told at an appropriate time," he told AFP news agency by telephone.
MPs from north and east Uganda, worst hit by the 17-year brutal rebellion, are boycotting parliament until the security situation improves.
They accuse the government and army of not taking the conflict seriously and of sending troops to DR Congo rather than to protect Ugandan civilians.
More than one million people have been displaced by the Lord's Resistance Army rebellion.
A committee investigating ghost-soldier related corruption in the army finished its work in August and its report is said to incriminate some senior army officers.