Students in cities across England could begin a mass exodus back to their families ahead of new lockdown measures coming into force on Thursday.
Hilary Gyebi-Ababio, National Union of Students vice president for higher education, said students were "really wanting to go home".
"There's a sense there could be a mass exodus," she told the BBC.
It comes after Universities Minister Michelle Donelan urged students, in a letter on Monday, not to "rush home".
Her message aimed to prevent these young people from travelling across the country to their families and potentially taking coronavirus with them, thus fuelling the pandemic.
Those in tier 3 restriction areas are not allowed by law to visit other households, which would include their family homes, but those in lower tier areas do not face the same restrictions until Thursday when the new lockdown rules come into force.
The NUS and the lecturers' union, UCU, have repeated a joint demand for all university teaching to move online, as much as possible, saying not to do so would cause a public health emergency
New government guidance published on Tuesday says some face-to-face teaching should continue.
'Ounce of certainty'
But thousands of students have spent several weeks of this term effectively locked down already, self-isolating due to real or suspected Covid-19 cases in their halls of residence.
Ms Gyebi-Ababio, 22, said: "We are really concerned about the the minister's statement, saying don't go home.
"It's not healthy or considerate to students."
She said students really wanted to do what was safe for others and right for them, and that it was important that they were allowed to have agency and make their own decisions.
She pointed out that the prime minister had said other members of the public could move to be in new households before the new lockdown measures come into force.
Many students did not have the usual support networks of friends, she said, or the formal support usually provided by universities, huge parts of which are closed.
"It's been really difficult for students - they do not have one ounce of certainty about what might happen."
She said the NUS was hearing from students who were "worried and confused right now", and this was only to be expected as they had not had any clear information.
"My younger brother is at university now, and I've had so many phone calls from him asking what he should do."
In some universities, students are reporting empty rooms in halls of residence which some students have already vacated.
Archaeology lecturer at University of Leicester, Dr Rachel Crellin, tweeted: "I've just taught: some students have been told to come home by their parents, some worried about being trapped alone in accommodation, others who don't want to take Covid home to vulnerable family and some who don't want to go home.
"This is causing chaos."
Ms Gyebi-Ababio said the government had talked weeks ago about a "mandatory two-week lockdown" to enable students to return home for Christmas but there were still no details about this.
She added: "After this four-week lockdown, students could be locked down for a further two weeks - that's a total of six. This could be really detrimental to their wellbeing and mental health."
Many students work while they study, to support themselves, but as in the previous spring lockdown, many had lost their jobs and were facing financial hardship, she said, and the government should have reflected on what happened then.