Kipsang claimed the world record when clocking 2hr 3min 23sec in the 2013 Berlin marathon.
He won the London marathon in 2012 and 2014, when he also won in New York, and he claimed bronze at the 2012 London Olympics.
It is not the first time he has fallen under the doping radar. In September 2014 he escaped punishment when he missed an out-of-competition drug test.
He risks a two-year ban for this latest infringement, if proven.
The development was the latest blow for Kenyan athletics ahead of the 2020 Tokyo Olympics as he joins the growing list of Kenyan athletes who have been suspended for doping offences.