The High Court has heard two VEC chief executives on salaries of over €100,000 had "taken the pain with everyone else", but were disproportionately adversely affected by a directive to cut a €12,500 allowance.

Galway VEC CEO Seosamh Mac Donncha and Mayo CEO Dr Katie Sweeney have taken a High Court action challenging the abolition of their Transport Liaison Officer Allowance (TLOA).

They say the allowance should not have been cut even though that part of their role ceased two years ago.

On the second day of the hearing, senior counsel Ercus Stewart said the State was relying on economic factors, but this argument was insufficient to dismiss his clients' case.

The effect on his clients was disproportionate to others, he said, adding they had "a serious complaint".

The application had been made in September and there was still no legislation and no change to the VEC Act.

He said the way in which the withdrawal of the allowance was done was "just a letter sent out saying this is withdrawn, the role ceased some months ago and your allowance has ceased".

There was ample precedent that people who have legacy allowances have been allowed to retain those allowances.

Counsel for the State Nuala Butler said it was fully accepted that Mr Mac Donncha and Dr Sweeney have given exemplary public service.

Ms Butler said the first indication that they were not happy was in August last year when the Department of Education got a solicitor's letter threatening litigation unless the allowance was restored and meetings regarding the deployment under the new educations boards were stalled.

She said Mr Mac Donncha and Dr Sweeney had up until then accepted their union SIPTU's position.

Ms Butler said the department said it could not negotiate individually on the matter.

At the opening of the case last week, the court heard they want the High Court to quash the department directive of June 2012 terminating the TLOA, which they claim was part of their basic pay.

They contend the allowances could not be withheld without a legal basis and it will also affect their pension entitlements.

The case against the Minister for Education and the State is taking place as the Government plans to abolish the 33 VECs and replace them with 16 new Educational and Training Boards.

Mr Mac Donncha and Dr Sweeney were described in court by their counsel as "reluctant litigants".

It is claimed Dr Sweeney faces being "ousted" from her present position and reassigned under the reorganisation, while Mr Mac Donncha will take over the running of three counties for no extra remuneration and will face a 300km commute.

The department claims the matters have been the subject of extensive negotiations through industrial relations mechanisms and it is implementing Government policy.

The High Court heard the TLOA was one of a number of allowances a CEO could earn.

The allowance was discontinued after the department decided to revamp the school transport system.

Mr Mac Donncha and Dr Sweeney are also looking for an order quashing the provisions of a departmental circular purporting to determine the categorisation of Education and Training Boards for the purposes of determining the pay scales applicable to CEOs.

The case continues tomorrow and judgment will be delivered on 29 May.