David Eaglesham, general secretary, warned that using such contracts would worsen long-term teacher shortages.
"We continue to be notified of attempts by some local authorities to implement fast-food style contracts for cover teachers, leading to huge differences in pay for teachers doing almost identical hours," he said.
This is a reference to the former practices of fast-food outlets requiring employees to wait around in readiness for work, but only paying them for the hours they put in at the counter.
Mr Eaglesham said: "Our view is, and always has been, that cover teachers should be employed for whole days and paid for whole days. Despite this, we still see teachers being pressured to accept work for only parts of a day, and even two separate parts within one day.
"All of this is carried out only in an effort to save costs and not for the benefit of young people. We call on all local authorities to revert to the original practice of employing teachers for a whole day or days."
He warned that cover teachers would become even more critical to the available pool of teachers in coming months and years because of the demographic profile of the teaching profession.
With large numbers of teachers close to retirement, the system would have to work doubly hard to maintain the number of teachers and increase it to the promised total of 53,000 by 2007, he said.
"If cover teachers are not properly paid, they are very likely to become disenchanted with either their employer or with teaching in general. Losing these teachers, many of them young teachers with a whole career potentially before them, will only compound the impending staffing crisis which will face our schools. Employers need to act now to avoid the spectre of part-time education and bonus schemes to attract new teachers," said Mr Eaglesham.
Meanwhile, the Scottish Executive has claimed "record numbers" of overseas teachers are "flocking to Scotland because of the excellent pay and conditions on offer".
The Executive said more than 1,400 teachers from outside Scotland registered with the General Teaching Council for Scotland in 2005 - up 40 per cent on last year. Almost 500 of these came from England, with Australia, Canada, New Zealand, and Northern Ireland making up the rest of the "top five" countries of origin.
Some 366 primary teachers have been registered, while in the secondary sector, teachers in English and maths (where the Executive aims to cut class sizes to 20 in S1 and S2) have figured strongly with over 80 and 60 registrations respectively. Biology with science, history and physical education make up the top five subjects for GTC "extraordinary admissions".
The GTC also reports 12 successful candidates coming into Scotland from Poland, and an increase to 19 of admissions from the Republic of Ireland. For the first time, a candidate from Venezuela and another from Lithuania have been admitted.
Peter Peacock, Education Minister, said: "We are determined to meet our ambitious targets to recruit record numbers of teachers. These figures....
show we are on track to reduce class sizes and ensure pupils continue to receive the highest quality teaching.
"Scottish education has an international reputation for high standards and teaching in Scotland has never been more rewarding. The pay and conditions are generous and, of course, the work is vital to the continued success of Scotland."