Uganda's players boycotted training on Tuesday because of a pay dispute, according to the country's Football Association (FUFA).
It is the latest of such disputes to break out at the 2019 Africa Cup of Nations following issues with Zimbabwe, Nigeria and Cameroon.
The Cranes finished second in their group and are preparing to face Senegal in the last 16 on Friday.
FUFA says the players are trying to "renegotiate" the terms of a deal signed between the two parties.
They claim the arrangement was agreed before the tournament and detailed the payments that had already been made to the players.
"As of 2nd July 2019, each player has received up to $14,600, with more daily allowances and winning bonuses awaiting to be earned," a FUFA statement read.