The wave design artwork was part of a Â£720,000 scheme to create a plaza outside the station.
A new statue of the Jolly Fisherman, the resort's mascot, is also being installed.
The sculpture was cordoned off in February 2012 after the accident.
Lincolnshire County Council now plans to install metal studs on the artwork to deter people from using it as a "playground".
But John Byford, from East Lindsey District Council, questioned why it had taken so long for the work to be done.
He said: "Tens of thousands of people still arrived by train to Skegness and that first impression counts.
"We have to have it right for them and it's not been right for nearly two years."
Colin Davie, from Lincolnshire County Council, conceded: "Quite honestly it's health and safety gone mad - this should have been sorted out a long time ago - but I'm pleased we've now got a solution."
The county has apologised for the delay and is coinciding the work with the installation of a new version of the Jolly Fisherman.
The mascot first appeared on a 1908 railway poster advertising the Lincolnshire coastal resort.
A sculpture outside Skegness rail station is to reopen to the public 21 months after it was closed when a boy on a bike was injured trying to ride over it.