Concerns have prompted the GTC to call on the Scottish Government to make a "clear statement" about the basic level of experience a teacher should have by the end of probation.
May Ferries, GTC convener, has also raised fears that the removal of ring-fenced funding to local authorities could jeopardise the financing of probationers' mentoring.
At its meeting this week, the GTC council raised concerns about the development of both routes open to probationers: the teacher induction scheme, set up under the teachers' agreement, and the alternative route.
The induction scheme was introduced five years ago to allow all probationer teachers to be considered for full registration within one school year. It was meant to guarantee a full year of training, rather than leave probationers struggling with various spells of supply work.
GTC council members want to focus on whether the allocation arrangements are as effective as they could be. They would like to review the number of "preferred authorities" offered; whether some of the larger ones should be split; whether the preference waiver scheme should continue; and whether the whole induction scheme is sufficiently flexible for new teachers with family commitments. It also wants to see greater consistency in the support for probationers, and better arrangements for teachers whose probation has to be extended.
However, its greatest concerns are over the 1,600-plus teachers who do their probation via the alternative route. While some have a similar experience to those on the main induction route, though at an independent school, others have to accrue experience on an ad hoc basis through supply, without the benefits of CPD or mentoring. Their experience is worse than in the old system, because they can only be employed on temporary contracts, says the GTC.
"Since the inception of TIS, the old route for completing probation has become the alternative route with the proviso that local authorities will only employ probationers on temporary contracts. Hence the alternative route in worst-case scenarios is, in fact, an even less attractive and lower quality experience than the old route," said Ron Clarke, professional officer for probation and CPD, in a report to the GTC's professional standards committee.
Teachers opt to take the alternative route for several reasons: some are unable to move from a particular locality to the allocated induction post; others wish to take longer than a year to do their probation more flexibly; and some want to work in the independent sector.
Of concern to Mr Clarke are the 801 teachers out of the 1,655 now taking the alternative route who have no choice in the matter - the foreign teachers who have come to work in Scotland.
He said: "While it could be argued that the alternative route should not be seen as comparable experience to the TIS, it must not be seen as such a poor alternative. Significant numbers of teachers are welcomed from other countries into the Scottish teaching profession by the GTC and can have a questionable probationary experience."
Mr Clarke has called for research into teachers' experiences of the alternative route to be carried out.