Crisis talks at Stormont Castle focused on major problems that hit parts of the Westlink, which were submerged below 20 feet of water.
The newly-opened Broadway underpass was said to be holding an estimated 20 million gallons of water.
Emergency services are continuing to clear the road, with extra police officers deployed to deal with Monday’s rush hour traffic, which threatened to grind Belfast to a standstill.
Major traffic problems seem to have been averted, however, the underpass will remain closed for the rest of today.
Weekend drivers on the Westlink were not so fortunate.
Many were forced to abandon their vehicles, with Road Service officials confirming as least five cars still remain below the water levels.
Yesterday the fire service worked to reduce water volumes, which it managed to condense by six inches every hour.
A spokesman confirmed the service was pumping 7,000 litres of water per minute from the road.
Facing criticism for response times, Minister Murphy explained such matters had to have a multi-agency approach, including privately-run organisations such as NIE and NI Water.
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Mr Murphy has ordered an investigation in to flooding at the underpass, where contractors were called upon to cut sections of the central barrier of the adjoining Westlink with angle-grinders to allow motorists to flee flood waters.
Meanwhile, homeowners across the Province are beginning to total up the cost of the floods, with the Environment Minister yet to decide on compensation rates.
Many are expected to receive emergency payments, like those who suffered serious water damage last year.
Those claimants were given £1,000 by the government to restore their homes.
However, Environment Minister Wilson has refused to set an amount for affected households this time around.
Mr Wilson said payouts would only be decided once the full impact of the flooding was clear.
Residential areas across Northern Ireland are still reeling from Saturday’s downpours, when a month’s rainfall fell in just 12 hours.
A government meeting of senior civil servants heard how rivers burst their banks, landslides occurred and many roads up and down the Province were cut off.
Police said two bridges had collapsed and 37 major roads were shut down, including part of the M1 motorway, and a train had derailed and the Fire and Rescue Service had helped people from their homes in Belfast, Counties Down, Armagh and Antrim.
Portglenone and Aghadowey were practically cut off, and there were several landslides, including one about one mile from the Spelga Dam on the Slievemaman Road in Newcastle, Co Down.
Newcastle Town Hall and the town's Presbyterian church were even opened as shelters for those affected by the floods, as was Watty Grahams GAA club in Maghera, Co Londonderry.
One of the collapsed bridges is at Fairy Glen, Rostrevor, Co Down and the other is on the Lurgan to Cahone road at Rathisland.
On Saturday night, the Northern Ireland Fire and Rescue Service said there had been ground-floor flooding in Belfast, Down and Armagh, and that every single one of its fire appliances was in use.
The Ballygawley Road and the Cookstown area of County Tyrone were among those flooded, and part of the Shore Road on the outskirts of north Belfast was closed after floods brought down a wall.
Sporting fixtures, including several Carnegie Irish Premier Division football matches, were also hit, and the Ulster Grand Prix at Dundrod, Co Antrim was cancelled.
(PR/NS)
