Hassan Omar, race coordinator, told The Associated Press: "This is an imposter. He is a guy who just showed up at the finish. He cheated to me and cheated to the timing chip."
He was questioned at the request of race officials but later released by police after no formal complaint was made. Police said he later admitted not running the whole race and that he'd said he hadn't intended to claim the prize money.
Njogu told reporters he had run the whole race, saying he became separated from the main pack of runners and found himself alongside half-marathon competitors.
"The group that I got lost with, we got mixed up with others from the 13 miles race," he said. "If I got lost, then we all got lost together, not just me."
However, Jared Ojuok, an inspector with Kenya Police headquarters in Nairobi, told NBC News that Njogu admitted not following the correct course.
"He was brought to the police station on the allegation that he participated in the marathon fraudulently," Ojouk said.
"When questioned he said he participated but his intention was not to win any prizes. He only wanted to finish the race and … told us that he told the official who was giving out the [winners'] tags that he was not running for the prizes. He himself indicated he was not following the right routes.
"Based on those facts, and because there was no substantive complaint raised, he was released immediately."