Primary teachers can take classes in secondary schools from today, when the Schools (Scotland) Code of 1956 is formally repealed - but the newcomers will be on probation until they prove themselves.
The Scottish Executive described the code as "outdated" and said its repeal would mean teachers will be able to move between sectors more freely.
It is anticipated that most of the primary teachers who do swap sectors will be used to teach classes in lower secondary.
Gordon Smith, president of the Association of Head Teachers in Scotland, said he hoped it would not mean consigning primary teachers to classes of pupils with learning difficulties, however.
"It should be about us in primary learning from secondary schools and using their skills in primary, and them using our skills in secondary," he said.
If the new flexibility simply meant primary teachers were used for learning support in S12, he did not think many would be interested. But if it allowed people to consider transition arrangements "where children don't leave the earth to go to the moon when they go from P7 to S1", and involved more interaction in teaching methodologies, the curriculum and team-teaching, then it would be welcomed.
Mr Smith added that he hoped the change would be a step towards a middle-school teaching qualification and called for reform of initial teacher education.
Bill McGregor, general secretary of the Headteachers' Association of Scotland, said secondary heads supported the move provided it did not mean a dilution of skills and was not used to get the Executive out of a fix.
"Where we have a concern is whether primary teachers are simply transferred to early secondary in order to fulfil targets such as reducing class sizes in the first and second year of English and maths," he said.
Mr McGregor also expressed fears that a primary-trained teacher working in junior areas of secondary might be sent to cover a middle-school class simply because there was no cover available. "We have huge concerns about that and it would need a different form of training," he added.
New Executive regulations replacing the code will incorporate a framework of professional recognition drafted by the General Teaching Council for Scotland.
In simple terms, this will ensure that teachers moving between sectors are appropriately qualified. Evidence of that qualification will be along similar lines to GTC procedures for checking exceptional admissions to the register.
A primary teacher taking lower secondary English or maths could, for instance, be granted conditional recognition as a secondary teacher. This would become full recognition after professional evaluation within a year or two.
The new regulations will also:
* ensure that a teacher suspended during an investigation cannot be employed in another authority;
* require authorities to employ adequate staff numbers;
* retain the requirement for all teachers to be registered with the GTC and for teachers of hearing and visually impaired children to have specialist qualifications.
Robert Brown, deputy Education Minister, said: "Our teachers are the jewels in the crown of our education system. They are professional, talented and an inspiration to many of their pupils.
"These measures help to reduce the bureaucracy and red tape about specific qualifications and introduce greater flexibility for teachers and schools.
They also ensure teachers will get recognition and better opportunities for continuing professional development, which will allow them to try out different aspects of teaching."