It is part of a 100-year plan for flood risk management around the estuary.
Plans for a flood risk management scheme are being considered and input from residents is being sought.
Mr Jones also emphasised that the board had been "spectacularly successful in terms of managing flood risk management".
Pete Fox, head of strategy and investment for flood risk management, says standing still is not an option.
This should be the focus of the new Flood Risk Management (Scotland) Bill.
"The design of the proposed flood risk management scheme is, on balance, considered to be acceptable, with regard to the impact upon the conservation area and the setting of adjacent listed buildings, " the council said.
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In a statement, the Department for Environment, Food and Rural Affairs (Defra) said it needed to "target funding for flood risk management where it will achieve the greatest benefit in protecting people and property from flooding".
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The spokesperson said last November the Welsh government published its first National Strategy for Flood and Coastal Erosion Risk Management to develop a flood and coastal erosion risk management system "fit for Wales and flexible enough to adapt to future changes".
The inquiry aimed to assess the Welsh government and flood risk authorities' progress in implementing the National Strategy for Flood and Coastal Erosion Risk Management.
The report ensures that the Environment Minister's department "will continue to explore opportunities to maximise investment on flood and coastal risk management".
The government's national strategy for flood and coastal erosion risk management recognises this.
The strategy, which outlines policies and a delivery framework on the risk management for flood and coastal erosion, was published in November 2011.
In the aftermath of 2010 floods, UNESCO has initiated a major project "Strategic Strengthening of Flood Warning and Management Capacity of Pakistan" for upgrading the flood forecasting and early warning system, and for the risk mapping of flood plains along the Indus River, in cooperation with the government of Japan.
Paul McKay, who chairs the council's risk, safety and emergency management board, said it was prioritising areas that were likely to flood or become isolated if the A6097 flooded.
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