Natfhe says it is concerned that the departure of Ivor Jones, after his post as the AoC's employment director was abolished, will weaken the organisation's capacity to speak for colleges on pay.
The unions were given a written assurance from the AoC during the summer that it remained committed to its negotiating role despite recent "restructuring", but Natfhe is still worried .
The AoC has agreed to meet the unions to discuss how pay talks will be carried out.
Barry Lovejoy, head of colleges at Natfhe, said; "We are very concerned about how these negotiations are going to continue. We hope this does not mean a shift towards a situation where colleges go their own way. We need more intervention, not less."
Sue Dutton, deputy chief executive of the AoC, who was responsible for pay talks before the restructuring, will take on a more direct role in negotiations.
The AoC will appoint an employment policy manager.
The vacuum created by this vacancy, and the uncertainty over the future of negotiations, comes at a time when Natfhe says a fresh outbreak of industrial action is looking increasingly likely.
A number of colleges have not implemented the current two-year pay deal - a situation which could lead to a series of nationally-co-ordinated local strikes in colleges.
John Brennan, chief executive of the AoC, this week reaffirmed the association's commitment to the present pay bargaining arrangements. He said: "We will have the capacity to deal with pay issues. It will be at a lower level than in the past but there will be full-time support from an employment policy manager. We don't think national pay bargaining is going to be disbanded."
Colleges would resist any calls for a review body similar to that which decides teachers' pay. He added: "I don't think that would find favour in the sector but I can't rule out any possibility over the longer term."
Mr Brennan said colleges are happy with the current process, which provides a "framework" rather than a binding agreement.
The AoC agreed the second half of the two-year pay deal in July after discussions with Natfhe, public-sector workers' union Unison, the Association for College Management (ACM), the Association of Teachers and Lecturers, the TGWU and the GMB.
The deal, which would bring lecturers close to pay parity with schoolteachers, was agreed in October 2003. It is said to be worth 6 per cent over two years, with a restructuring of the pay scales.
The second year of the agreement provides a starting salary of pound;20,283 for qualified lecturers and job evaluation which involves unions as well as employers.
Reacting to the news of Sue Dutton's more hands-on role, Peter Pendle, general secretary of the ACM, said: "She can be tough but so can we."