"A vigilante came after 9pm on Wednesday night. Next morning I saw them gone when I was helping a new mummy duck cross the road" he wrote in a post to a local community page.
He said a neighbour saw the signs being taken down on a security camera.
A friend and a fellow duck protector told Lupton his sign was found in Glen Eden, a neighbouring suburb.
Lupton was in discussion with the Auckland Transport to get permanent signs placed in the area.
When asked whether Auckland Transport had denied Lupton's for permanent signs to be placed in the area the manager for West Auckland said "no, this is new".
Council team manager compliance response Max Wilde said it's not uncommon to see ducks on the road at this time of the year.
"Our bylaw [Signage Bylaw 2015] is in place to make sure signs are safe, consistent in their messaging, don't cause a nuisance and keep Auckland looking good."
Wilde confirmed the Council had received a complaint as the signs "had not been approved by Council".
Lupton told the Herald he has bonded with the ducks, with one family often sleeping outside his house.
Lupton has made new signs to put up in the same place where they were taken down.