The Tamil Refugee Council has claimed at least 11 of those on board have been tortured by Sri Lanka's intelligence services.
Labor opposition immigration spokesman Richard Marles slammed the government's operation.
"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.
The injunction comes ahead of a visit to Colombo this week by Morrison for talks on illegal immigration. He is due to meet top officials from President Mahinda Rajapakse's government.
The interim injunction from a late-night sitting applies at least until a hearing resumes on Tuesday afternoon and was granted after lawyers argued the transfer was illegal.
Refugee advocates claim the asylum-seekers have been deprived of the ability to have their claims for refugee status properly assessed, wit