Athletics Kenya has suspended Rosa Associate and Volare Sports for six months pending investigations into doping.
There are however fears that the move could hurt the careers of famous elite athletes under the Italian and Dutch stables.
The national federation accused the two firms of being responsible for the surge in doping cases in the country.
At least 36 runners, including three times Boston marathon champion Rita Jeptoo, have tested positive for banned substances in recent times.
Rosa closed their female marathon training camp in Kapsabet recently over doping allegations subjecting all athletes in their camp to dope testing at an Eldoret Hospital.