The clinic opened from 8am to 10am this morning, with booster jabs offered to people aged 50-69 and healthcare workers.
Today was the first day that those aged 50-59 could receive the booster, provided five months had passed since their second dose or three since receiving the one-shot Janssen vaccine.
This led to a queue of over 200 forming at the UCD walk-in clinic. Many were turned away as the HSE announced the clinic had run out of vaccines.
Those who left without receiving the booster were advised to Wicklow's Shoreline Leisure Centre instead, where a clinic is in operation until 5pm this afternoon.
HSE National Director Damien McCallion advised people to keep an eye on the HSE's social media platforms for updates on which vaccine centres were experiencing queues.
"There’s a range of centres… if people see that there are queues in one area, they may be able to decide to go to an alternative centre or wait until those queues abate over the day," he said.
The queuing chaos comes as Tánaiste Leo Varadkar claimed the booster programme is set to be expanded to those aged between 30 and 49 before Christmas.