Faults in the system responsible for vehicle height detection, fire suppression mechanisms, CCTV and emergency lighting, led to the closure of the tunnel on 27 February causing traffic chaos in the city.
HGVs making their way to Dublin Port were forced to divert through the city centre.
A National Roads Authority (NRA) spokesman said there were, "serious concerns about the durability and reliability," of the safety system and could not guarantee that there would not be further traffic disruption caused by more closures to the tunnel.
He added that the NRA would now be pursuing the tunnel contractor, a Nishimatsu-Mowlem-Irishenco consortium, for "several million Euros" compensation to rectify the fault in the operating system.
"We will be enacting certain elements of the contract relating to service levels," he said. "We will give them ample opportunity to offer us satisfaction."
An NRA letter sent to the consortium last week said: "We have been repeatedly reassured and guaranteed that the tunnel systems would be fully fit for their intended purpose and that the installed equipment would be both durable and resilient. We have had a number of significant equipment malfunctions. We put you on notice that we are taking legal action to recover all costs arising from deficiencies in the equipment that you have provided."
The tunnel closure is the latest controversy to hit the £570M project that opened in December 2006 £228M over budget.
The tunnel consortium is also seeking further payments of £76M from Dublin City Council for completion of the project. The claim is currently in arbitration.
A spokesman for Carillion, which will handle claims following its acquisition of Mowlem in 2006, refused to comment on the latest claim but pointed out that responsibility for operating the tunnel safety system rested with a separate company appointed by NRA called Transroute.