According to Dodger spokesman Josh Rawitch, when Dodger lawyers filed for bankruptcy, the team's accounts were frozen for 48 hours.
Any employees whose checks bounced were reissued checks on Wednesday. Rawitch also said the team is reimbursing the affected employees with any bank fees they were charged for the bounced checks.
It is unclear how many Dodger employees were affected.
A source familiar with the Dodger finances told ABC7 that they were not sure whose check would bounce, so when they found out some had bounced, they alerted everyone.
In bankruptcy court in Delaware, the judge allowed the team to draw an initial $60 million to maintain operations, which included Thursday's payroll.
MLB is looking into the possibility of taking the team away from owner Frank McCourt, saying in a statement that he was "obviously unable to distinguish between his personal interests and those of the club."
Baseball's constitution allows MLB Commissioner Bud Selig to take control of a team that seeks Chapter 11 protection, but the league first must file a motion seeking termination of the franchise. There is no timetable for that filing.
Frank McCourts ex-wife and former Dodger CEO Jamie McCourt described the bankruptcy filing as disappointing. She said that Frank McCourt has a "rule or ruin philosophy."