Fife Council claims to be more than pound;1 million adrift in the current financial year alone under the teacher induction scheme. It is to write to the Scottish Executive to call for a fairer allocation of funds.
Smaller authorities in the central belt, such as East Renfrewshire, have seen their funding allocation for probationers rise significantly.
James McKinstry, the council's senior manager (resources), said: "Fife has got the same five national educational priorities to deliver as other authorities. To do that, we should got an equitable share of resources."
John Stodter, general secretary of the Association of Directors of Education in Scotland, said that the gap occurred once authorities had received their initial allocation of probationers, for which they receive 40 per cent of funding from the executive.
Since the executive guarantees to give every probationer a year's induction, it then provides 100 per cent funding for these surplus probationers to be allocated a place.
However, probationers had to be given some choice in where they spent their induction year, and more rural authorities with disparate populations tended not to attract applications. With more mature entrants coming into teaching, many with family ties that restricted their mobility, the central belt attracted the lion's share of fully funded places.
"If you are in an authority where you are struggling to get staff anyway, this situation can seem unfair," Mr Stodter said.
Fife this year asked for 74 fully funded placements but was told it would only receive 26. Instead of receiving 6.94 per cent of the national total of funds available, it has to do with a 2.71 per cent share.
A national total of pound;30 million is retained by the executive to finance probationers' places in full. The difference in the way funds are allocated amounted this year to a deficit of pound;1.05 million to Fife.
Senior managers fear further losses of up to pound;200,000 will be incurred if probationers drop out of their guaranteed year.
At the end of last session, Fife was only able to offer 80 out of 138 probationers permanent posts. But Mr McKinstry hoped this situation would improve through retirements and departures.
A spokesman for the executive said: "We think it is important that newly qualified teachers get the chance to reach the standard of full registration in one year. We want to offer every newly qualified teacher a job in their first year.
"We do not, however, believe in forcing teachers to go to a place they don't want to go to. We give them that flexibility. We do not have 72 extra probationers to send to Fife. The scheme was designed to match demand with supply."
According to Fife's figures, a total of 15 authorities have suffered a reduced share of funds due to revised budgetary allocations, with falls ranging from 6.38 per cent in Glasgow to 0.5 per cent in Perth and Kinross.
Meanwhile, Fife also claims, East Renfrewshire has gained to the tune of 5.79 per cent.
A spokesman for the Convention of Scottish Local Authorities said that, despite the winners and losers, the allocation of probationers was fairer than ever.