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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.
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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.
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The previous instances were all resolved without any disruption to the ongoing tournament.