German media say the move followed some creepy clown ambushes in Germany like those in the US and UK. In some cases the terrified victims were injured.
But the Deiters fancy dress store is still selling such masks.
German Interior Minister Thomas de Maiziere warned there would be "no tolerance" of creepy clown attacks.
"When people face threats of violence on a wide scale, it can be treated as an offence," he said, referring to the clown hysteria. "It no longer has anything to do with harmless Halloween traditions."
He said it was "no joke" when pranksters terrified people by brandishing chainsaws or knives.
The clown panic began in August, in the US state of South Carolina, with locals reporting people in clown masks trying to lure children into the woods.
Fuelled by social media, the craze spread to the UK and incidents were reported in some other countries too.
The German department store chains Karstadt and Galeria Kaufhof have stopped selling "creepy clown" masks in the run-up to Halloween.