The German track has been shut down for three months after a horse tested positive for an equine infection of the blood.
All horses based at Cologne cannot leave the racecourse, including the Peter Schiergen-trained Danedream, a brilliant winner of the Longchamp feature 12 months ago.
Colonge racecourse general manager Benedikt Fassbender told Press Association Sport: “It’s a nightmare.
“We are the biggest training centre in Germany and one horse has tested positive for equine infectious anaemia (EIA).
“For three months we are now in quarantine – no horses can come in to the track, and no horses can come out.
“It is a disaster, especially as Danedream cannot take part in the Arc at the orders of the special vets.
“Danedream has not been infected by the disease, but every horse will be tested for the infection in the next few days.”
Patrick Barbe, racing manager for Danedream’s part-owner, Teruya Yoshida, said he was “very pessimistic” about Danedream being given clearance to compete in the Arc.
He said: “At the moment, Danedream is very well and has not been infected.
“The only horse who has been infected is on the other side of the racecourse to Danedream.
“Because the Arc is only now in a few days’ time, I’m very pessimistic she will be allowed to run.”
Meanwhile, Teddy Grimthorpe has confirmed Sea Moon as a likely runner in the Prix de l’Arc.
The four-year-old, trained by Michael Stoute, was last seen finishing fifth when sent off favourite for the King George VI And Queen Elizabeth Stakes at Ascot in July, but was only beaten a little over two lengths.
Grimthorpe, racing manager for owner Khalid Abdullah, expects Ryan Moore to be in the saddle.
Moore has been sidelined by injury since late August and his comeback date has yet to be confirmed, but Thursday will be the earliest he can return.
Moore has been linked with the ride aboard Derby hero Camelot, who will require a new jockey if he does line up due to Joseph O’Brien being unable to make the weight of 8st 11lb.