The Government should have considered other options before stripping a university of its right to admit foreigners, critics have said.
More than 2,000 students could face ejection from the country after the Government revoked London Metropolitan University's highly-trusted status (HTS) for sponsoring international students.
The move, which critics said sent a damaging message that the UK deports foreign students to all corners of the globe, comes after more than a quarter of students sampled studying at the university did not even have permission to stay in the country.
Professor Eric Thomas, president of Universities UK, said there were other ways to address UK Border Agency concerns and the university's licence should only have been revoked as a last resort.
"We believe that there were alternative ways of addressing UKBA's concerns, and that revocation of a university's licence should only be a decision of last resort," he said. "We will be working with UKBA to ensure that compliance issues can be addressed in a more constructive way in the future."
London Metropolitan University's HTS status was suspended last month while the UK Border Agency (UKBA) examined alleged failings.
Immigration minister Damian Green said that along with more than one in four students sampled not having permission to stay in the country, a "significant proportion" of students did not have good English and there was no proof that half of those sampled were turning up to lectures.
The move could mean more than 2,000 students being deported within 60 days unless they find another sponsor, according to the National Union of Students.
Professor Malcolm Gillies, vice chancellor at London Metropolitan University, described the claims made against the institution as "not particularly cogent" and said it would be disputing them.
He said the university had set up a hotline for those affected on 020 7133 4141 and would try to help them find places at other universities.