Scottish education minister Brian Wilson has instructed SHEFC to be "flexible" if institutions under-recruit next session.
Mr Wilson said concern about tuition fees and maintenance grants had been "overstated". But SHEFC should show flexibility.
His letter to SHEFC chairman Sir John Shaw, says: "I appreciate that the forthcoming changes to student support may cause some short-term variability in student flows. In order to maintain institutional integrity for students currently in the system, I attach great importance to policies that encourage institutional stability."
Mr Wilson has also told SHEFC to "preserve the viability of the small specialist institutions", a clear message to the Royal Scottish Academy of Music and Drama and the art colleges that they need not feel pressurised into mergers.