A new sequence of lights near the Dublin port entrance of the Dublin Port Tunnel caused a 2km (1.2 mile) tailback on its first full day of operation.
Lorries were backed up to the port from the entrance to the tunnel yesterday morning when the early boats arrived in.
The National Roads Authority (NRA) said the problem was caused by drivers continuing to drive towards Dublin city centre rather than through the tunnel, which takes them to the M50.
The Dublin Port Company said the situation, which was at its worst between 5am and 7am yesterday, had been a "total mess" and blamed it on light sequencing that went against traffic leaving the port.
Its chief executive, Enda Connellan, said: "It was because the phasing of the lights leaving the port was only 15 per cent for the port. The lights weren't even synchronised.
"We expect some teething problems but I suppose the frustrating part of it is the amount of time it takes for people to actually react when things go slightly wrong."
Just 46 per cent of all trucks leaving the port used the tunnel yesterday, though that figure is likely to increase.
There was no repeat of the problems during yesterday's evening rush hour.
The Irish Road Haulage Association (IRHA) said many drivers had been "spooked" by the overnight closure of the tunnel for tests and had not used it because they had mistakenly believed it was still shut when the ships arrived in yesterday morning.
"It was a combination of confusion, misinformation and the fact that there is a lot of business in Dublin city centre at this time of year," said Jimmy Quinn, spokesman for the IRHA.
"I expect that figure to improve over time."
Lorry drivers caught up in yesterday's traffic jams said two sets of lights near the entrance to the tunnel caused all the problems. Truck driver Donnie Rowllins said it had been "total chaos".
"Nobody was going anywhere. I wanted to go through the city to get on to the N4 and I had to divert on to the M50.
"The drivers kept getting caught because when one set of lights changed to green the other changed to red."
Patrick McGill, who arrived from Holyhead at 6am yesterday, said: "It took me an hour and 10 minutes to get from the Stena boat to the entrance to the tunnel. From what I heard, it got a lot worse than that.
"Within the docks, every road was chock-a-block this morning. It was bumper to bumper with lorries. I saw a mile queue at least.
"We couldn't even get to the tunnel. The delay was in getting there. The lights this morning were a complete mess."
The NRA said the problem arose because lorry drivers had not used the tunnel.
A spokeswoman said: "Traffic coming from the ships on to the quays usually gets priority with the lights, but now priority is with the traffic going through the tunnel. The sequencing of lights on the city North Wall quays reflects that, but a lot of drivers were using the old routes.
"We expect that to change over the next few weeks."
Large trucks are banned from the city centre from February 19th next year.
The NRA also confirmed that the tunnel will continue to close between 11pm and 4.30am for tests for a couple of weeks.
