Uganda's players boycotted Africa Cup of Nations training on Tuesday because of a pay dispute, according to the country's Football Association (FUFA).
It is the latest such dispute to break out at the tournament, 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 say the players are trying to "renegotiate" the terms of a deal signed between the two parties.
They say the arrangement was agreed pre-tournament and detailed the payments that had already been made to the team.
The players have yet to comment.
Nigeria, Zimbabwe and Cameroon have all had similar situations either in the build-up to Egypt 2019 or since it has started.
All those situations were resolved without significant disruption to the tournament.