Interac spokeswoman Caroline Hubberstey says the problem is mainly affecting deposits, but a few financial institutions are having problems sending funds.
Hubberstey says most people are able to send an Interac e-Transfer but when the notification for deposit arrives at the receiver, the receiver may be unable to deposit the funds.
Hubberstey said Tuesday night that Interac was working to resolve the issue and hoped to have systems restored soon.
She says the service is affected across the country and the problem was first noticed on Tuesday morning.
She says all other Interac services — Interac Debit, Interac Cash and Interac Online — are operating normally.