Spokeswoman Caroline Hubberstey said the problem mainly affected deposits, but a few financial institutions were having problems sending funds.
Hubberstey earlier said most people were able to send an Interac e-Transfer but when the notification for deposit arrived at the receiver, the receiver was unable to deposit the funds.
Several people took to Twitter to express concerns that payments for such things as rent may not go through or of being hit with NSF charges.
Interac replied that these issues ”should be cleared up” by users’ financial institutions in the morning.
Hubberstey said the service was affected across the country and the problem was first noticed Tuesday morning.
She says all other Interac services — Interac Debit, Interac Cash and Interac Online — were operating normally.
Interac also offered ”sincere apologies" on its Twitter feed for the "inconvenience this disruption caused.”