One northbound lane of the M8 between Cahir and Mitchelstown remains closed as a precaution while gardaí and maintenance staff monitor local conditions.
The motorway was closed in both directions last night, between junctions 11 and 12, after both northbound lanes flooded and the southbound section was used for council and maintenance company vehicles as they worked to clear the water.
There were reports of motorists being stuck in the area for up to two hours.
Diversions were put in place taking traffic away from the motorway at either end of the blockage and onto the old Dublin-Cork road through Skeheenarinky.
The southbound lanes were re-opened later last night and one northbound lane has also been opened, allowing traffic from both directions to progress.
However, the northbound "slow" lane is still closed as workers try to ascertain the cause of last night's flooding.
It is believed the excess water came from nearby hills, close to the Galtee Mountains.
Investigations are under way to see if there is a blockage in a local stream or other water course, which diverted water down to the road.
Gardaí from both Cahir and north Cork were present at the scene last night, but say that there is sufficient capacity on the motorway today to allow anticipated traffic levels through in both directions.
Director of Motorway Network Operations for Transport Infrastructure Ireland, Kevin O'Rourke, said one lane was sufficiently adequate for the traffic capacity this morning.
Speaking to RTÉ's Morning Ireland, Mr O'Rourke said it appeared that flood water from the Galtee Mountains got onto a local road network and travelled along local roads before entering the motorway near a bridge.
He added that it could be something as simple as a tree high up in the hills blocking a culvert that is causing the problem.