The massive flood defence system, aimed at protecting Venice’s lagoon during high tide, was finally installed in October.
But on Tuesday the system failed to swing into action because the forecast erroneously predicted a rise of only 1.2 metres above sea level.
“To activate MOSE a bigger forecast is necessary,” Venice Mayor Luigi Brugnaro told the Italian news agency Agi.
“We will have to review the rules of the command post.”
As the weather worsened, city authorities sent out alerts to residents warning them to be prepared for flooding.
The barriers take several hours to raise, and by the time it was clear how high the tide would be, it was too late to take action.
Flooding reached a high of 1.37 metres above sea level in the afternoon.
The waters drowned St Mark’s Square – the Renaissance city’s lowest area at about one metre above sea level – and invaded the famous basilica as many shopkeepers blocked their entrances with wood panels to keep the water out.
Officials said a meeting would be held later on Wednesday to “analyse what happened yesterday and, if necessary, make significant changes to the procedures applied up to now for MOSE”.
The long-awaited MOSE system, which was given its first full test in July, was praised for saving Venice from recent high tides.
In early October, MOSE’s huge yellow floodgates, which rise to separate the Venetian lagoon from the sea, succeeded in shielding the city during its first real-time test when the high tide rose to 1.2 metres.
The system again functioned successfully a few weeks later in preventing water of up to 1.35 metres from entering the lagoon.
The MOSE dams were designed in 1984 and were supposed to come into service in 2011, but progress was blighted by a corruption scandal and cost overruns.
The Italian government came under pressure to finally finish the €6 billion project, which is designed to protect Venice from tides of up to three metres, after the city experienced its worst flood since 1966 in November last year.
The flood killed two people and caused an estimated €1 billion worth of damage to monuments, businesses and homes.