The news is contained in a communication to all members from the trustees of the joint Irish Aviation Superannuation Scheme.
The scheme handles pensions for employees in all three companies, although SR Technics has now closed.
In it, trustee Brian Duncan says that because of the 0.6% per annum deduction from the pension scheme, the trustees will have to make what he called "modest benefit reductions".
Pensioners will be advised in due course of how the cuts will be implemented.
Mr Duncan notes that between March 2011 and the end of 2011, the deficit in the IASS scheme rose from €343m to around €700m due to disappointing investment returns and lower interest rates in European countries.
While the deficit may have reduced slightly in the meantime, the position remains very volatile.
Talks are underway at the Labour Relations Commission in a bid to agree a strategy to address the deficit.
The talks are crucial because the Government cannot sell its stake in Aer Lingus until the deficit issue is addressed.
Mr Duncan says that current employer and employee contributions are not sufficient to fund benefits.
He also informs members that employers have said that they will not pay additional contributions into the scheme.
Strategies to reduce the deficit include payment of additional contributions, cutting the benefits of those who are currently working and those who have left but deferred their pensions, and the purchase of sovereign annuities for pensioners.
Mr Duncan's document also raises the issue of co-ordination with the State pension.
At present, staff in the scheme who stay until the normal retirement age do not cost the scheme the full price of their pension, as it is offset by the State pension.
However, those who leave early are entitled to both the full pension from the scheme, and the State pension on top.
That has placed an additional burden or strain on the pension scheme.
The DAA pointed out that the operation of the pension scheme was a matter for the trustees of the scheme.
The Director of Human Resources at Aer Lingus, Michael Grealy, said the letter was welcome in that it clarified important issues regarding the pension scheme.
The Chief Executive of the Labour Relations Commission, Kieran Mulvey, who is chairing the talks, said he would be recalling the parties at the earliest possible agreed date in a bid to accelerate progress in the negotiations.
He said he also wanted to avoid further speculation on the issue.
