In an email to staff on 7 July, Malcolm Gillies writes that the university must reach its total intake target of 4,873 students in 2011 to be in good shape for 2012, when London Met will charge the lowest fees of any university under the new regime.
"If we fail to recruit to our target, our future sustainability as a university could be at risk," he says.
A London Met spokeswoman said that the number of clearing places would not be known until A-level results were released on 18 August, "however, we estimate around 2,000 places might be available".
Sir Alan Langlands, chief executive of the Higher Education Funding Council for England, delivered a warning at a meeting of the London Met governors in March.
According to the minutes, he said: "Hefce's role in the turbulent times ahead for higher education would not be to bail out universities."
London Met must repay £30 million to Hefce over the next three years after it wrongly claimed public money by reporting inaccurate student-completion rates. The problems occurred before Professor Gillies was appointed vice-chancellor.
The university attracted fierce criticism when it cut its course offering in preparation for 2012, shutting subjects such as history, philosophy and modern languages.
Professor Gillies says that the university, which has pitched fees as low as £4,500 in some subjects, must be "affordable" and that cross-subsidy of courses is no longer an option. His critics argue that the university, which has the highest proportion of working-class students in the country, is closing off arts and humanities subjects to those students.
London Met's spokeswoman rejected the possibility that the controversy might deter potential students from entering through clearing: "We made a decision to reduce our undergraduate course offering from 577 to 160. We will still be recruiting the same number of students to these, more popular, 160 courses."