"Australia's international obligations are reliant upon a credible processing system and we have deep concerns about how that could have been performed by video link at sea in a way which gave an individual assessment, when all the time the boat was steaming towards Sri Lanka," he said.
Morrison's statement came days ahead of a visit to Colombo this week for talks on illegal immigration.
He is due to meet top officials from President Mahinda Rajapakse's government on Wednesday and will also participate in a ceremony to hand over a patrol boat Canberra has gifted Sri Lanka.
The boat is expected to be used to patrol Sri Lankan waters and halt vessels leaving the country with asylum-seekers bound for Australia. Concern had been mounting over the fate of two boats reportedly intercepted by the Australian navy in Australian waters late last month.
There were claims that Australia could be breaking international law by screening them at sea and returning them involuntarily to a country in wh