Athletics Integrity Unit said in a statement that a charge was issued against Wanjiru for "use of a prohibited substance/method", but the Kenyan said he was clean and had never used doping.
Kenyan Daniel Wanjiru, the 2017 London Marathon winner, has denied any wrongdoing after he was provisionally suspended for an Athlete Biological Passport (ABP) violation by the sport's independent Athletics Integrity Unit on Tuesday.
The AIU said in a statement that a charge was issued against Wanjiru for "use of a prohibited substance/method", but the Kenyan said he was clean and had never used doping.
His management company Volare Sports said the charge by the sport's independent AIU was based on "alleged abnormal variations in the haematological profile" in Wanjiru's ABP.
ABPs are used to monitor selected biological variables over time that indirectly reveal the effects of doping rather than attempting to detect the substance or method itself.
Under anti-doping rules Wanjiru, 27, is barred from competing until a hearing has taken place into the allegation.
"I am clean in the sports I do," he was quoted as saying in a statement issued by Volare Sports. "I feel I am already seen as a sinner of doping, but I am not. I am innocent.
"I stand for clean sports. My results of the past came through hard work only. I have never used doping," he added
"We are currently investigating the case. Knowing I have never used anything, I have faith everything will be all right."
Volare Sports said no prohibited substance was found. "The accusation is based on an assumption," it added. "We are already trying to get to the bottom of this in order to find the truth."
London Marathon CEO Nick Bitel said if Wanjiru's result was voided, they would recover the prize money paid out.
"At this point the athlete is provisionally suspended and due process needs to be completed by the authorities," he told Reuters.
"If the results of any athlete who has competed in the London Marathon are later voided by a doping finding, we will take action to try and recover any money paid to the athlete, so that those other athletes whose results are enhanced can benefit."
Ethiopia's Kenenisa Bekele finished second in the 2017 race, nine seconds behind Wanjiru.
Susan Kamau, chief executive of Athletics Kenya, declined to comment on Wanjiru's case.
In addition to his 2017 London win, Wanjiru secured gold at the 2016 Amsterdam Marathon and has finished eighth and 11th in the past two London marathons.
Kenya is world famous for its dominance in long and middle-distance running, but over the last five years a series of doping scandals has tarnished its reputation with around 60 of the country's athletes sanctioned for anti-doping violations.
In December, Kenya's government said it was planning to impose criminal penalties - including possible jail terms - on athletes caught doping.
Last year, Kenyans Asbel Kiprop, Cyrus Rutto and Abraham Kiptum were given four-year bans, while Vincent Kipsegechi Yator received the same suspension earlier this month.
Wilson Kipsang, the former marathon world record holder and bronze medallist at the 2012 Olympics, was provisionally banned in January for whereabouts failures and tampering with samples.