Ricardo David, the immigration commissioner, said his office was co-operating with a probe being carried out by a special government task force on trafficking, which could lead to criminal charges or the firing of officers.
"We assure the public that this bureau under my watch will not tolerate these shenanigans," Mr David said.
A total of 19 immigration officers, who were found to have helped illegal recruitment agencies, were dismissed from their jobs last year, Mr David added.
The labour ministry has said gullible Filipinos from poor provinces have been duped into travelling to Syria, many of them women who end up employed as maids under very poor working conditions.
It said an average of 100 Filipinos were entering Syria every month.
The Philippine government banned Filipinos from working in Syria and ordered a mandatory evacuation of its nationals there in December, some 10 months after an uprising against the rule of President Bashar Al Assad broke out.
Out of almost 7,000 Filipinos known to be in Syria, some 1,500 have already been successfully repatriated, the labour ministry has said.