"If you talk to athletes candidly, you get the feeling that doping is going on in these camps," he told Reuters by telephone from Eldoret.
Kiptanui, who won three world titles between 1991 and 1995, is the first high profile former Kenyan athlete to allege the African nation's runners are using performance-enhancing drugs.
He said the fluctuating performances of some Kenyan athletes were enough to arouse suspicion.
"They run well today and just (flop) the following moment. Surely, something is not right," the 42-year-old said.
Kiptanui said catching drugs cheats was difficult because they doped for specific races and the drugs could not be traced the following day.
Allegations that Kenyan athletes were using drugs surfaced ahead of the Olympic Games last year when German television broadcaster ARD reported systematic doping by Kenya's elite athletes who train in running camps in the Rift Valley region.
Athletics Kenya rejected the accusation and angrily accused the broadcaster of attempting to distract its athletes ahead of the London Games where Kenya performed dismally.
Kenyan officials said in May they would investigate the claims, while World Anti-Doping Agency president John Fahey visited Kenya last year following the ARD documentary and held talks with Kenyan government officials.
Athletics Kenya secretary-general David Okeyo rejected the claims by Kiptanui and challenged him to provide evidence.
Okeyo said action was taken against athletes caught doping.
"One of the athletes who failed a doping test during last year's national championships was suspended and it is public knowledge. We also have suspended a few more athletes," Okeyo told Reuters.
"So to suggest that we are not taking action against those caught is not only malicious, but totally slanderous."
Athletics Kenya officials told Reuters that over the past 12 months four Kenyan runners have failed doping tests, including Jemima Jelagat Sumgong, the runner-up at the Boston marathon, and Rael Kiyara, who won the 2012 Hamburg women's marathon.
Mathew Kisorio, a former African junior champion in the 5,000 and 10,000 metres, tested positive for an anabolic steroid after the Kenyan championships last June while Ronald Kipchumba failed a drugs test following the Linz marathon in Austria. (Writing by Drazen Jorgic; Editing by James Macharia and John Mehaffey)