Rotherham United and Huddersfield Town's Championship relegation rivals hit with points deduction
It means the Latics are now eight points adrift of safety in a Championship relegation battle involving Huddersfield Town and Rotherham United.
Wigan were sanctioned for failing to pay their players on time on three occasions last year – in June, July and October.
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Hide AdAs a result, they reached an "agreed decision" with the Football League in January which would trigger the deduction instantly if they were late with payments again this season.
In a further breach, owner Abdulrahman Al-Jasmi has failed to deposit 125 per cent of its forecast monthly wage bill in a designated club account as the Bahraini businessman has blamed delays in processing overseas payments in the past.
New charges have been laid against the club for non-payment of players wages and not complying with the agreed decision. Al-Jasmi will also be charged with misconduct.
Huddersfield are three points from safety with eight matches to play.
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Hide AdRotherham are 20th, four points ahead with a game in hand. Cardiff City, who sit between them, have a point fewer with nine matches left after Saturday's Rotherham v Cardiff game was abandoned because of a waterlogged pitch.