He denies the allegations and is being held in custody before he returns to court within a fortnight.
"If my husband knew about this I don't know what he would do to that foreigner," one mother told Cebu Daily News afterwards.
Munro was the head of the Zhuhai International School in China until last month, and formerly a teacher and boarding master at a prestigious boys' school in Melbourne, Victoria, SMH reports.
He has been a regular visitor to the Philippines since 2011, usually staying for 21 days, police allege.
They followed him after a tip-off and found boys aged nine, 10, 11, 12 and 14 in his hotel room at the Stakili resort.