The Gills had agreed to sign defender N'Gala, 27, after he left Eastleigh.
However, he played for Barnet and Eastleigh earlier this campaign, and rules state a player cannot appear for more than two teams in one season.
But National League club Dover say they have been allowed to sign him following talks with the Football Association and English Football League.
N'Gala started his career at West Ham, and had spells at Stevenage and Portsmouth before joining Barnet in 2014.
He became Eastleigh's record signing when they bought him from the Bees in November.
The Fifa Players' Transfer rules came into force this season, and recently led to Leyton Orient winger Ulrich Nnomo's proposed move to Paris FC being cancelled.
Find all the latest football transfers on our dedicated page.
Bondz N'Gala has joined Dover, a week after a move to Gillingham fell through because of Fifa regulations.