Teachers advising pupils on further study have only just been made aware of the new requirements and a number have complained that they will have to provide personal statements and academic references for pupils at a busy time of year to meet the first deadline of December 15.
The ongoing accreditation of the University of the Highlands and Islands has led to the change which will also mean schools have to pay extra administration fees of between pound;5 and pound;14, depending on the number of applications for courses.
Pupils used to be able to apply to local colleges directly. But the UHI began negotiations early last year for UCAS membership and has only recently been told its application has been successful.
Jane Plenderleith, UHI curriculum development officer, said she appreciated the problems schools might face but UCAS membership had advantages.
"This gives us an entry into the UCAS handbook for the year 2000 and details the courses available for students. There are still procedures in place for local students to be able to make late applications directly to the local college of their choice, but there could be problems. Places on the desired course might not be available. The UCAS application means that they can apply to other educational institutions as well as to UHI."
Dr Plenderleith added: "I have some sympathy with teaching staff who feel the procedure was finalised rather late in the year, but UHI is dependent to some extent on good communications being maintained between the schools and the colleges.
"This gives us huge advantages in processing data on each student and it also gives a very quick turnaround with applications and reminders to students to confirm and finalise details. It also gives UHI access to a wider student base and we can attract students from all over Britain and the rest of the world."
It appears information has yet to filter through to some secondaries in the Inverness area.
Derek McGinn, head of Culloden Academy and past president of the Headteachers' Association of Scotland, said staff were "gobsmacked" that the change had been announced at so little notice. Careers officers were particularly affected.
"This is causing quite a bit of irritation," Mr McGinn said. Staff had already taken senior pupils through the background to filling in the UCAS form on the advice they thought applied. Now that will have to be altered. "We are going to have to go back to youngsters and say nobody knew about this," he complained.
Culloden pupils who would have applied direct, for example, to Inverness College, will now have to go through UCAS and probably incur a pound;15 fee. The school has not yet decided who is going to pay.