When Scottish Government education secretary Michael Russell sits down today to make his New Year's resolutions, Larry Flanagan has a suggestion for his list: a return to collective bargaining on pay and conditions for college lecturers.

As the general secretary of the Educational Institute of Scotland (EIS) points out, lecturers at further education (FE) colleges in Scotland find themselves in an anomalous position. It is costing some of them nearly £5000 a year. For while school teachers and those working in the higher education sector (universities) enjoy the benefits of national pay bargaining, salaries and working conditions have been negotiated separately at each of Scotland's 41 FE colleges since they were spun out of local authority control and became independent 20 years ago. Significant disparities in remuneration, holiday entitlement and the like have developed in the interim.

To the casual observer, the persistence of this quirk is puzzling. A return to national bargaining in the sector was an SNP manifesto commitment in 2011. The policy is supported by Labour and the National Union of Students, as well as the EIS. And the Griggs Review of FE Governance last year not only recommended such a move but even set out a detailed timetable, with a mechanism for harmonisation to be agreed by August 2013.

Furthermore, the radical restructuring of FE colleges into 12 regions makes such a move both logical and desirable. As each regional board has to agree pay and conditions, it makes sense to move to national agreements, eliminating anomalies and duplication of effort. Indeed, atomised bargaining arrangements are increasingly indefensible.

The elephant in the room is the fact that this harmonisation process is being conducted at the same time as the sector suffers very deep cuts to its learning and teaching budgets: 10% in each of the last two years with more to come. Some college principals, their feathers already ruffled by their loss of autonomy, clearly fear the cost of harmonisation will result in even more damaging job cuts and students will suffer.

Colleges have had a bad year. Budgets and student numbers are down, despite increases in application numbers and rising long-term youth unemployment. Surely there is an argument for the Scottish Government putting its money where its mouth is and funding the cost of the transition to national bargaining if the alternative is even deeper cuts in staffing levels.