Department of Foreign Affairs (DFA) officials said the Filipino sailors were implicated in the case for having acted as guarantors in the loan secured by Indian national Stanley Pereira, the chief accountant of their company.
The names of the sailors were not available.
Pereira reportedly defaulted in paying back the loan amounting to eight million dirhams, prompting lender NBRAK Bank to file the complaint.
Pereira lured the Filipino seamen into acting as guarantors by promising them 1,000 dirhams each in commission.
The sailors, employed by Gac Marine, were arrested while their ships were docked in Abu Dhabi.
Pereira reportedly repaid half of the loan following his arrest.
A court in Abu Dhabi had ordered the release of the seamen from the Al Wathaba Central Prison in the UAE capital, but the bank filed a motion to block implementation of the decision.
Pereira has reportedly admitted that he secured the loan without any intention of repaying it, and leaving the guarantors to face the consequences.