At one point the underpass stretch of the Westlink motorway was flooded with around 20 feet of water.
City-bound traffic was only reopened today, with the country-bound route expected to be accessible later, according to the Roads Service.
Highway Management Construction Project Director, Leo Martin, said the weekend's heavy rain proved an "extraordinary event".
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Mr Martin said: "To get a month or three-quarters of a month's rain in 12 hours is fairly exceptional rainfall,
"No doubt the culvert did its job, it was designed and built exactly in accordance with specifications and put into practice.
"But unfortunately you can't countenance for severe weather conditions like this."
Water is still lingering in the underpass, which has now turned to mud and sludge. Mr Martin said workers were continuing to clear the debris.
Stormont Executive Ministers are holding talks today, and are expected to receive an update on clean-up progress.
Traffic on the Westlink has continued to flow without major delay.
However, flooding on the railway line at Portadown has caused disruption to the Enterprise service.
Roads Minister Conor Murphy has recommended an investigation into the underpass flooding goes ahead.
(PR/JM)
