Wigan were deducted three points in March by the English Football League for failing to pay salaries and were charged this season for late payments in June, July and October.
"Staff wages were paid on Friday with the Chairman, Mr Talal Al Hammad, making a decision to pay as many employees as possible within the organisation with the resources available," Wigan said in a statement.
"All remaining playing and non-playing staff will be paid at the earliest opportunity following the Bank Holiday weekend...
"All first-team players have been given the day off from training today given the difficult circumstances."
Wigan spent eight seasons in the Premier League before they were relegated in 2013, the same year they won the FA Cup.
They are bottom of the Championship and will be relegated at the end of the season. Their final game is against Rotherham on Monday.
