Engineers proposed putting barriers 30m (98ft) tall on the seabed at three entrances to the lagoon. The barriers would only be raised during flooding, about a dozen times a year.
Experts believe the level of the Adriatic will rise 30cm (12ins) over the next 100 years, which means the frequency of high tides will be "catastrophic" without the barriers.
The government last month rejected the plan, called Project Moses, saying it might turn the Venetian lagoon into a stagnant pool, cut off from the Adriatic. The MIT team was retained to assess its environmental impact. But it endorsed the plan and said construction should start quickly. The pounds 1.4bn project would take 10 years.
The experts said the gates would actually increase circulation in the lagoon and improve water quality. The Environment Ministry has no alternative proposal.
MIT members said conclusions of the Italian Environment Ministry panel that rejected Project Moses were "untenable and supported by no scientific evidence". (AP)