After several years of upheaval in the further education sector in Scotland, there is a new crisis.

Managers at Edinburgh College are planning to "harmonise" staff contracts, which means the creation of a uniform set of conditions for all staff and a single pay scale. In some cases, according to the EIS union, it also means lecturers ending up with lower pay and poorer conditions.

The response of the union to the plans has been robust, with lecturers at Edinburgh going out on strike this week. The union also says it is determined to persist with the industrial action until management has a rethink on the plan.

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The problem for the management is that the merger which created Edinburgh College in 2012 threw up anomalies that, in come cases, left colleagues doing the same job in the same department but on different salaries and conditions. The union believes that, in trying to solve the problem, managers have embarked on a race to the bottom. In other words, harmonisation means deterioration.

In reality, what has happened is the management of Edinburgh College has been left trying to fix a problem that first emerged 20 years ago when colleges were taken out of local authority control. Disparities in pay and conditions have developed ever since and the merger process and budget cuts have only made those disparities more obvious.

The Government's argument all along has been that some of the budget cuts will be offset by the rationalisation of FE (of which the creation of Edinburgh was part) and, to some extent, that makes sense. Unnecessary management should be cut; back-office functions should be shared; the duplication of courses in the same area should be removed.

However, the rationalisation process has also started to create problems such as the ones seen at Edinburgh College, problems the Scottish Government should have anticipated. It is the Government that has been driving the merger process by cutting the budget but it has left the colleges to deal with the consequences.

The upcoming return to collective bargaining for colleges, passed into law last year, may help improve the situation. There is no good reason to deny collective bargaining to colleges when it is already in place for university staff and teachers, although it will also mean the unions will be in a position to demand national action. In the longer term, what collective bargaining offers is the possibility of fairly removing the anomalies seen in Edinburgh and preventing rationalisation unduly damaging pay and conditions (although it may already too be late for Edinburgh College itself).

The Scottish Government deserves credit for supporting collective bargaining, but it also has to take responsibility for the effects of its policy on colleges. Scotland's FE sector has a critical part to play in addressing the country's skills shortage, particularly in the emerging and growing sectors of the economy. However, colleges will be only able to do that if shrinking budgets do not also mean shrinking morale, and poorer conditions, for their lecturers.