"Normally it would take three to six months to plan an operation like this and we pulled this together in 24 hours," NSW Police Commissioner Mick Fuller said.
Mr Morrison said the recently returned Australians should be thanked for co-operating with police and army officers.
"I know this is a terrrible inconvenience for you but it is necessary to save lives and we thank you for your co-operation," Mr Morrison said.
About 350 defence force personnel are helping enforce the isolation.
"We will treat these people with absolute respect and dignity but we will need their support," Mr Fuller said.
"The 14 days, I am sure, will be a challenge for them and perhaps the food is not up to standard or they feel that the bed is not as comfortable as their own.
"They need to understand that we are trying to protect the community of NSW."
Thirty people who arrived at Sydney Airport on Sunday are being tested for coronavirus after reporting respiratory symptoms.
"They've undergone coronavirus testing which takes six hours, so they'll remain in that higher health testing area and higher level of isolation until we get to the bottom of it," Mr Fuller said.
NSW Health Minister Brad Hazzard on Sunday slammed a group of medical professionals who, after returning by plane on Friday from South America, allegedly ignored directives to self-isolate in hotels.
A number instead flew to their interstate homes.
"I'm bitterly disappointed they chose to ignore a safety measure for themselves and others - they are the people who you would expect to know better than anyone else," he said.
Meanwhile, Australians who were on board the Norwegian Jewel cruise ship and placed in compulsory quarantine earlier this week in the Swissotel in Sydney have been critical about the handling of the policy.
"We were totally unaware we would be held here against our will and forced to stay in a hotel, rather than go home to our home," Cathy Poole, 72, told SBS News on Saturday - her third day under guard at the hotel.
"The food is not palatable, it is cold.
"There are no fresh towels, no cleaning being done!"
Australia has 3,873 COVID-19 cases, with the majority in NSW - 1,791. That figure includes 207 people with an unidentified source of transmission, indicating local transmission is growing. Sixteen people have died from the virus.
Additional reporting: AAP