They estimate that they will be landed with a pound;1 million bill as their share of the pound;6 million that will be raised by the charges if the proposals go ahead.
Tom Kelly, chief executive of the Association of Scottish Colleges, said:
"We want a pricing structure that is much more transparent and fair, and we also want to see this transfer of resources met by a corresponding transfer of cash."
The major issue for the colleges is that the SQA proposes to load the same levels of increase on to National Qualification units as it will on courses.
This hits colleges disproportionately, the ASC argues, because many FE students take units without sitting the external exam.
Mr Kelly asked: "The increases in charges are to cover the SQA's increasing costs which are generated by courses. So why should those who take only units have to pay for a service they do not get and subsidise others?"
The association also wants a distinction made between the costs of producing units which are part of the national assessment bank and those which are locally developed and which the SQA merely validates.
The plans as they stand will see unit prices in National Qualifications such as Intermediate and Higher rise from pound;4.75 for each entry to pound;6.50 by 2005-06. Courses at these levels will see the SQA charge rise from pound;23.75 to pound;32.75 over the period. These represent hikes of 37 per cent for units and 38 per cent for courses.
Mike Haggerty, the SQA's director of communications, said all parts of the authority's catalogue would have to play their part in helping it reach break-even point from its present deficit funding of pound;18 million.
"Courses will still be run at a loss even with these increases and units will still be run at a loss even with these increases," Mr Haggerty said."We want to get to break even on every single element of our catalogue and then we can start to think about differentials."
The SQA, he continued, recognised there were relativities which is why the proposed increases for national certificate and diploma courses are much lower - 10 per cent over the two years. The ASC has welcomed that, although it is concerned at the suggested rises for Scottish Vocational Qualifications which are of the same order as for HN courses.
The colleges believe the Scottish Executive, which has approved the new charges, should meet the added costs because its policies have led to huge financial burdens for the SQA - fuelled largely by the 240 per cent increase in the number of courses with the introduction of Higher Still.
The SQA has promised to review the tariff regime planned for 2005-06, and says that any change will not lead to higher rates. But Mr Haggerty warns:
"We are trying to recover a position that is four years old."