Health Minister Chris Baryomunsi said that Agha Khan Hospital in Nairobi had agreed to take only 400 out of the 17 000 Ugandan patients who needed radiotherapy care.
Baryomunsi said they would airlift only the most serious cases to Nairobi, Daily Monitor reported.
He advised the remaining 16 600 patients to go for palliative care or use morphine to relieve pain.
Uganda has only one radiotherapy machine, which according to the BBC, was donated second-hand to Mulago Hospital in 1995. The machine was said to have undergone several repairs.
The machine broke down last week, but efforts to fix it failed, with members of parliament threatening to block government officials from seeking cancer treatment abroad until the machine was replaced.