The bulk of the work on the 212-tonne structure, which protects more than 17,000 properties in the city, was completed last summer, but the towers are again covered in scaffolding while its windows and window frames are replaced.
The project, the first overhaul of the barrier in its 30-year history, is expected to be finished by the end of October and will not affect the operation of the barrier.
Work began in 2009 and has mainly been carried out over the summer months when there is less danger from tidal surges.
Improvements have also been carried out, including the installation of a new drive mechanism – which lifts and lowers the barrier – while every bolt and rivet on the steel gate has been checked and replaced if necessary.
The barrier, which is the second biggest in the UK and has become a landmark on the city’s skyline, was built in 1980 in response to the last severe tidal flooding to hit Hull, in 1969.
The barrier protects the city from tidal surges, which occur when low pressure in the north of Scotland causes winds which push great volumes of water south along the East Coast.
The effect is magnified in river estuaries, particularly when combined with spring tides. The barrier is used on average about 12 times a year and can be deployed within half an hour of a flood warning.
The agency has called the barrier a “vitally important tool” in protecting people, homes and businesses.