But in March the district council claimed new data, gathered by its senior officers in conjunction with Niwa, had come up with an entirely different scenario that showed the Waipoua River in particular would not only handle a one in a 100-year flood but would likely cope with double that.
In the latest move the district council has shifted its ground to say Masterton is protected to the level of a one in 50-year flood.
MDC and GWRC now agree that due to the increased risk of extreme weather and challenges caused by climate change, extra protection is needed to "ensure ongoing protection into the future".
According to the joint councils, the initial focus will be on assessing and upgrading any potential weak points in the town's flood protection, which might not meet the base 50-year protection level.
This focus will provide information on the benefits and feasibility of staging future upgrades, in order to spread the cost.
The district council's chief executive Pim Borren said the two councils are most effective in the community "when we are working together towards common objectives".
"We have different responsibilities in terms of flood protection and land use, but share the one clear objective of ensuring that our community is adequately protected from the risk of flooding both now and in the future."
The regional council will be carrying out further development work on options in coming months through its Floodplain Management Plan process.