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The body, angry over flagging results in the past few years, summoned 200 athletes to a training camp two months ago ahead of the World Indoor Championships in March and the London Olympics in July and August.
But Bekele and other athletes including Olympic women's 5 000 and 10 000 gold medallist Tirunesh Dibaba ignored the call-up, technical director Dube Jilo said.
"We have banned 35 athletes, including Kenenisa and Tirunesh, from competing in any event," he said.
"It has been two months now since we summoned every athlete in contention, but this group has so far failed to respond."
He said the ban would be reconsidered as soon as the athletes reported for training.
Bekele, who has yet to decide if he will compete in London anyway, was not immediately available for comment. Neither was Dibaba.
The 29-year-old Bekele, who had not raced on the track since 2009 because of injury, dropped out of the 10 000 metres at last year's world championships in Daegu, South Korea, after 10 laps.
However, he was back to his best at the Brussels Diamond league meeting later in the season, setting a year's best for the 10 000.
For years a powerhouse in long-distance track events, Ethiopia has lost ground in recent years with local commentators concerned by a lack of talent coming through the ranks to replace the likes of the great Haile Gebrselassie.
After a disappointing World Championships in Daegu, the country's athletics chiefs decided to revamp their preparations for upcoming events.
"There is a lack of commitment, and our preparations haven't been up to standard so far," Dube said.
"We have to distinguish who is in good shape ahead of events."
