One of the two urine samples also had two sets of DNA, Hajo Seppelt said on his ARD channel programme, quoting sources close to the inquiry led by Canadian lawyer Richard McLaren that looked into the Russian doping.
Seppelt produced the ARD documentary in 2014 that set off inquiries into Russian sport and led the International Association of Athletics Federations to suspend Russia.
The IAAF only said that "new information" about Klishina's case had led to its decision.
Seppelt quoted his sources as saying that the two tampered bottles could have been opened "illegally".
The McLaren inquiry said the Russian sports ministry and Russian secret service switched samples in bottles at the 2014 Sochi Winter Olympics.
Russian sports minister Vitali Mutko on Sunday slammed the IAAF as "inhuman" over the surprise ban of the 25-year-old long jumper who has insisted that she is "clean".
"Some provocative moments are premeditated," he added.
"I don't even know how to describe (the IAAF decision), I don't even know how people can do that, it's inhuman," Mutko told RIA Novosti agency.
Russia has denied any state involvement in doping. The opening qualifying round for the women's long jump starts in Rio on Tuesday.
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