The Civil, Public and Services Union (CPSU) is blaming the Department of Foreign Affairs and Passport Office management for the chaos at the Dublin office.
Union General Secretary Blair Horan said the pre-planned closure of the counters was mishandled by senior management.
The Department of Foreign Affairs said the backlog of passports has risen to over 50,000 as a result of the industrial action by CPSU members.
But Mr Horan, speaking at the union's annual conference in Galway, is defending his members' action.
"Management did not do anything to prioritise the queue which took place outside the passport office last Friday," Mr Horan told delegates.
He said management had refused to close the door of the office at any occasion and there was a flood of applications still in the building when the offices actually closed.
"As far as we are concerned it was an absolute mismanagement by Foreign Affairs that caused the chaos in the passport office last Friday."