Researchers in Ukraine say that the population may be in decline because poachers have been removing the animals faster than they are breeding.
Thirty-one horses were taken from a Przewalski's horse reserve and from a local zoo.
They were released into the zone in 1998 and 1999.
Scientists from the state-run SSSIE Ecocentre in Chernobyl say the horses were introduced to "enrich the biodiversity" of the exclusion zone surrounding Chernobyl nuclear power station's damaged nuclear reactor.
The zone was evacuated in 1986 after reactor number four exploded.
Professor Tim Mousseau, a biologist from the University of South Carolina who visits the zone to work at least twice a year, says that the herd he has spotted has been "getting smaller" in recent years.
Continue reading the main storyA readily available supply of horsemeat is tempting for people”End Quote Professor Tim Mousseau University of South Carolina "Many people in this part of Ukraine are very poor," he told BBC Nature on a recent trip to the exclusion zone.
"So access to a readily available supply of horsemeat is tempting for people."
But Sergiy Paskevych, a researcher from the National Academy of Science in Ukraine and the author of a website dedicated to ecology and wildlife in the exclusion zone, told BBC Nature that poachers probably travelled long distances to the exclusion zone and took the carcasses away to be sold.
Mr Paskevych explained that the most recent data on the horses suggested that there were 30-40 individuals in the zone. This represents a severe decline in their numbers from a maximum of 65 animals in 2003.
"It is difficult to say what [factors] affect the lives of these animals," he said.
"Maybe it's the wolves - there are a lot of its in the exclusion zone - or maybe it's disease.
"Of course, the anthropogenic factor [of hunting] cannot be excluded."
Igor Chizhevsky, a biologist from Chernobyl's Ecocentre who studies the zone's wildlife, said that poaching could be affecting the wild horse population there.
Mr Chizhevsky confirmed that Ukrainian researchers had found several dead horses that had been shot by poachers. He added that it was difficult to determine how many horses were now left.
"For three years, no one has counted the population," he told BBC Nature.
Biologist Zbyszek Boratynski captured this footage of the wild herd close to an abandoned farm in the Chernobyl exclusion zone"So we don't know."
Mr Paskevych suggested that the zone should become a reserve "with a research centre for the study of nature and radioecological consequents of nuclear disaster".
"But today, the exclusion zone is not a reserve, and there are almost no scientists [with the] knowledge and ability to explore the area," he said.
"In the current situation... the future of Przewalski's horses is very vague."
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