Chinese students were also questioned in Melbourne and Brisbane.
University officials reported that some students had been questioned for hours, had food withheld and their luggage removed.
Detained students unhappy with treatment
Universities Australia chief executive Catriona Jackson said she had raised the issue directly with Home Affairs Minister Peter Dutton and is hoping that an official apology is forthcoming for those who were poorly treated.
"We have good solid reports from university officials who say people are very distressed," she told ABC Radio.
"They are very unhappy with the way they have been treated. They have been kept in what they regard as detention for a period of time without adequate food. Some have had their clothes taken away, we understand.
"This is not the way to treat people who are coming here in absolute good faith."
She said some students were concerned that their visas had been cancelled based on the information received from Border Force officers. She said it is important that Chinese students affected receive accurate information.
"[Some of them have been told or believe their] visas are suspended. They are not cancelled. They won't have to re-apply for their visa. They won't have to pay a fee again.
"We're after accurate information for these students. Not stuff that makes them understandably even more frightened than they already are, coming from a very distressing situation."
She said Mr Dutton had promised to "act on that [the cases] with all haste".
"I think it would be appropriate in some cases for an official apology to be issued to them... These people are distressed, they are coming from a country that has a really serious epidemic on its hands.
"We must make sure that we are treating these people with the compassion we would expect ourselves if we arrived in a country in similar circumstances."
A statement from Home Affairs said the Border Force Commissioner and staff appropriately exercised their discretionary powers, adding that visas solutions were being considered for those caught up by the travel ban.
"The health and welfare of the Australian community is the Australian Government’s highest priority. This includes all people in Australia of all nationalities, including citizens, permanent residents and temporary visa holders alike," the statement said.
"The Australian Border Force Commissioner has used his discretionary powers to provide border clearance to a number of individuals to allow them to enter Australia.
"For most people, this occurred at the airport.
"Others were placed in an alternative place of detention – serviced apartments – while their case was assessed.
"All of these individuals undertook health screening and were counselled to self-isolate for a period of 14 days, in the same way as others who are exempt from the enhanced border control measures.
"The ABF and the Department is working with impacted individuals to discuss future visa options."
Darren Shen from Jiangxi province has told SBS News his friends were among those turned away at Sydney Airport on Saturday evening.
He says the whole episode was confusing and disappointing for those told to return to China after arriving in Sydney.
"They [Border Force officials] asked them to return home immediately. They feel disappointed because they just want to study.
"They're healthy. They didn't go to Wuhan this year. And they are far away from the city. But they have been refused to get into Australia. They cannot go study.
"It is a waste of their money. They need to buy two or three tickets."
The Chinese Embassy in Canberra said it was unhappy with the treatment of Chinese students at Australian airports, saying there was not enough time to alert students who were already in transit on flights when the travel ban came into effect.
"It was quite chaotic," said Chinese Embassy Deputy Head of Mission Wang Xining.
"We are not happy about the situation because they were not alerted. There was not enough time to be alerted about the restriction."
'Welfare absolutely paramount'
Higher Education Minister Dan Tehan met with the Universities Australia board on Monday night, after meeting at lunch time with a taskforce formed to ensure Australia's reputation is managed during the bushfire crisis and the Wuhan coronavirus outbreak.
He said flexible study arrangements would give Chinese students the option to study online or remotely, whether they are self-isolating for the fortnight incubation period, or have returned to China.
"The welfare of all students - whether they are here in Australia or whether they are overseas - would be absolutely paramount.
"We have all committed to provide maximum flexibility to ensure those students who remain offshore are doing everything we can to ensure that they can either: study online or study remotely."
A petition asking the University of Sydney to push back the start date two weeks to 9 March has already collected 4,000 signatures.
The petition started by the University of Sydney Representative Council argued a delayed start would reduce the academic pressure faced by students who cannot attend class due to the travel ban.
About 189,000 Chinese international students are enrolled in Australia's tertiary sector. Of that number, 155,000 study in Australia's universities.
In the 2018-2019 financial year, the international education sector generated $37.6 billion for the Australian economy, an increase of $5 billion on the year prior.