The Cranes who finished second in their group are supposed to be preparing ahead of their encounter with Senegal on Friday, July 5.
A statement from the country's Football Association (FUFA) said 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.
"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 statement read.
"We hope the players will rescind their decision and report for training on Wednesday," a FUFA spokesman told the BBC.
This is the latest such dispute to break out at the AFCON tournament in Egypt, following issues with Zimbabwe, Nigeria and Cameroon.
The previous instances were all resolved without any disruption to the ongoing tournament.