According to the Samoa Observer, there have been reports that both the Malietoa Tanumafili II Hospital at Tuasivi and the Safotu District Hospital have run out of the cards.
Hospital staff say new supplies were not expected to reach Savai'I until Tuesday, the first day of the school year.
Minister of Education Loau Keneti Sio said he would make enquiries to find a way to resolve the matter.
A weekend media release made no mention of the card shortage but did say the public were well-informed of the new Infants Amendment Act regarding school registrations.
It said evidence of immunisation is now a compulsory requirement for all school children for enrolment in any school.
Principals who knowingly enrol children without complete vaccination records face fines of up to $US3700.