Freeze branding is commonly used in Australasia and North America.
The petition started at the Hanoverian approvals in Verden and will be continued at the Trakehner and Holsteiner approvals, the Trakehner Verband said.
In an open letter to Ilse Aigner, minister for nutrition, farming and consumer protection, the associations ask that the arguments of breeders be considered before a final decision on hot branding is made.
Calls for the ban have been prompted by the introduction of compulsory microchip identification, and breeders, who say branding is a traditional way of identifying their progeny, want to use hot branding as an additional identification method.
European Union law requires horses to be individually identified.
On October 15 the Federal Government was asked by welfare groups to draft a law to ban hot branding. The Trakehner Verband said that research into hot branding had been "very unfair and not objective". It said the issue dealt with "the fundamental question of whether horse breeders are animal abusers."
It said that "animal activists" see hot branding as an "unnecessary cruelty to animals and thus a violation of the Animal Welfare Act."
The Verband said that hot branding on the hindquarters of foals was quick, and "little more ... than a simple insect bite".
"The hindquarter is the most muscled body region in foals and thus largely insensitive. Immediately after branding the foals are back to normal.
"The many years of practical experience shows that foals being hot branded show no 'substantial pain, suffering and damage', for it is relatively stress-free and gentle."
The Trakehner Verband said claims that the hot iron is pressed on the horse for several seconds are false. "Further, the insertion of the microchip is described as causing much less pain, suffering and damage than hot branding. This does not coincide with the observations in practice," the Verband said.
"After the first year of using the microchip, we find that this method is much more stressful for the foal."
The Trakehner Verband says that microchips were not tamper-proof, and there was only a small pool of people nationally who had access to readers for identification purposes. It also questioned the health risks for the horse.
"As a tool for identification of the horse ... (it is) questionable. The small scar at the point of identification is a natural reaction of the tissue, however, the transponder is a foreign body, which is a long-term risk to the health of the horse."
However, a study in Denmark in 2009 found that hot-iron branding was more painful than inserting a microchip. Researchers at the University of Copenhagen compared the behavioural and physiological responses of seven horses that were subjected to both hot-iron branding and microchip insertion, and concluded that hot-iron branding should be abandoned wherever possible.
Scotland also banned hot branding this year, with a government official saying: "There is no place for hot branding in a country which prides itself on its high animal welfare credentials."
The British Equine Veterinary Association and the British Veterinary Association both said at the time that a ban was necessary on welfare grounds.