The plan will need approval from parliament. Flooding the polders is a sensitive issue for the Netherlands, where a catastrophic flooding killed 1,850 people when dikes were breached by freak high tides in 1953.
A Dutch authority temporarily halted plans to deepen and widen the Westerschelde estuary in July, after conservation groups objected to the project, arguing the area was a unique region where mud and sandbanks attract many migratory birds.
The government hopes the new plan will meet the concerns of the environmental groups and convince the authority, the Dutch Council of State, to allow work to deepen the river estuary to proceed.
Plans to deepen the Westerschelde, an estuary for the Scheldt river, are aimed at easing access for large cargo vessels to Antwerp port, Europe's third largest container port based on 2008 figures.
Delays to the dredging work have strained Belgian-Dutch relations, which led some Belgian politicians to call for a boycott of mussels from the Netherlands earlier this year.