The extension, which will run in tunnels for 76% of its 211.3km length, is due to open in the 2030 financial year.
The additional works to raise line speeds will add an estimated Yen 12bn ($US 110m) to the cost of the project and primarily involve redesigning tunnel portals and raising noise barriers.
The measures are expected to reduce Shin-Hakodate-Hokuto - Sapporo journey times by around five minutes compared with 260km/h operation.
The initial 148.8km phase of the Hokkaido Shinkansen from Shin-Aomori to Shin-Hakodate-Hokuto opened in March 2016.
East Japan Railway Company (JR East) hopes to introduce a new generation of high-speed trains based on its 360km/h Alfa-X prototype on the Tohoku and Hokkaido Shinkansen from around 2030.
Earlier this month JR East announced plans to upgrade the Joetsu Shinkansen for 275km/h operation.