The province says inspectors intercepted two contaminated boats this summer — one from Ontario and one from New York — that were carrying the invasive species.
Another 99 of the 2,500 boats inspected were deemed high risk.
That means they were coming from states or provinces that are either infested with mussels or don't do inspections and monitoring.
Environment Minister Robin Campbell says only 50 per cent of boaters are stopping to have their watercraft inspected and stricter measures may be necessary.
Zebra and quagga mussels are almost impossible to eradicate once they take hold and can cause millions of dollars in damage by clogging pipes and hurting aquatic life.
In addition to regular inspections at weigh stations, Alberta joined forces with Montana in a pilot project this summer using sniffer dogs to detect mussels on boats.
Manitoba spread potash at four harbours on Lake Winnipeg earlier this year to try to eradicate the species, but some anglers say larvae are still being found.