Track superstar Bekele was on world record pace and looking strong at halfway during Sunday's race but then dropped back dramatically before staging a superb recovery to finish second behind Kenya's Daniel Wanjiru.
He later said that his problems had been caused by blistering from new shoes and that he had to change his running style to enable him to pick up his pace.
It was thought at the time that triple Olympic champion Bekele was wearing Nike's new Zoom Vaporfly Elite shoes, which will be worn by Eliud Kipchoge, Lelisa Desisa and Zersenay Tadese in their attempt to run a sub-two-hour marathon in Italy next month.
However, Nike said on Tuesday that Bekele was wearing their Zoom Vaporfly 4% shoes and that the Vaporfly Elite were being used only by the three Breaking2 athletes.
"As he has done in previous marathons, Bekele ran in the Zoom Vaporfly 4%, in which he set an Ethiopian record and the second-fastest time in history on a record-eligible course in Berlin," a spokesman said on Tuesday.
"We are working closely with Bekele to understand what happened."
(Editing by Sudipto Ganguly)
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