Homeless families may not be housed in modular homes by Christmas as the contractor has pulled out of the site due to protests this week.
Martin McCloskey, managing director of Western Building Systems which is building the first tranche of 22 prefabricated houses in Ballymun, said that he took the decision on advice from his security staff.
Around a dozen protesters blocked work on Thursday morning and a smaller group turned up again yesterday blocking the entrance to the site but had left by mid afternoon.
"The deadline is in real jeopardy at the moment," Mr McCloskey said.
"We have a programme with works scheduled to be completed by December 21, manufacturing is still on-going in our factories, but the site dilemma has really left us in the complete unknown at the moment.
"I'm not saying there'll be none ready - there may be some - but I doubt it," he added.
The Tyrone-based contractor does not expect to return to work on the site until Tuesday at the earliest.
Mr McCloskey said that a larger crowd turned up at the site overnight after the first day of the protest, prompting his security team to raise the alarm about safety on the site.
Protesters were demonstrating in a bid to secure a refund of €5,000 that they had paid more than a decade ago for co-op housing that was due to be built on the site.
Work is underway to come to a new agreement with the council to ensure that those who paid originally will get either a house or a refund, despite the modular homes being erected on the site.
A meeting of the O Cualann Housing Alliance, which has since undertaken the co-op plans, and Dublin City Council (DCC) is due to take place on Monday to iron out an agreement to allow the co-op to progress.
DCC said that work would recommence accordingly and that they would be engaging with the contractor to secure a prompt return to work over the weekend.
Meanwhile, Environment Minister Alan Kelly, who has spearheaded the project at Government level, has urged all parties to resolve the matter urgently so that work can begin on the site.