UEFA said in a statement on Friday it had lifted the suspension of prize money for 16 of 23 clubs originally targeted in September after they wiped out arrears owed to other teams, their staff or tax authorities.
However, Qatari-owned Malaga, who have qualified for the last 16 of the Champions League in their debut season, failed to meet a deadline of end-September to show they had cleared overdue payments.
Their case has now been referred to UEFA's adjudicatory chamber that has a range of sanctions available including disqualification from current competitions.
A Malaga spokesman said the club were working to settle debts "as soon as possible" and hoped to "unblock" the situation with UEFA very soon.
He also noted that midfielder Duda, one of the club captains, had said on Thursday that he and the players were satisfied with the guarantees they had received.
UEFA is introducing Financial Fair Play measures designed to force European clubs to balance their books. Clubs could face exclusion from European competition from 2014-15 onwards if they do not curb their losses.
Other clubs facing further action are Croatia's Hajduk Split and Osijek, Romania's Rapid and Dinamo Bucharest and Partizan Belgrade and Vojvodina of Serbia.
Poland's Lech Poznan and Arsenal Kiev of Ukraine also face action. They were not among the clubs originally targeted but their overdue payments situation deteriorated between June and September 2012.
After heavy investment to reach the Champions League, Malaga appeared to run into financial problems at the start of the season, delaying payments to players and selling others.