Marathon runners Wilson Erupe Loyanae and Nixon Kiplagat Cherutich will serve two-year bans, while Moses Kiptoo Kurgat was suspended for a year.
A fourth athlete, Francis Kibiwott, who finished 45th at the 2007 world half marathon championship in Italy, was cleared after his case was reviewed by the medical commission of world athletics governing body the IAAF.
The east African nation, famed for its middle and distance running prowess, has been on the defensive following reports of widespread doping among its elite athletes.
"Loyanae is a top marathoner who is in the top 30, but we will not spare anyone," said Athletics Kenya secretary general David Okeyo.
"We are taking doping seriously. But in most of the cases in this country, like Kiplagat's, they say that they are sick.
"We have been telling them (athletes) that when they are sick, they should let us know what (medication) they are being given so that we can present their cases since the rules are very clear," he added.
Earlier this month, three-times world 3,000 metres steeplechase champion, Moses Kiptanui said doping took place in Kenyan running camps and similar allegations were made by German television broadcaster ARD before last year's Olympics.
Athletics Kenya have rejected the allegations.
"Those are the athletes we have banned in the past two months. But that still does not mean doping is widespread among our athletes," said Okeyo.
"We have nothing to hide. As soon as we establish any athlete has doped, we shall expose them.
"The procedures involved require a lot of time and the athletes must state their case before the medical commission so the issue of AK not taking any action does not arise."
- Sports & Recreation
- Athletics, Track & Field
- Athletics Kenya
- Francis Kibiwott