The 37-year-old Ethiopian, who recorded a fastest ever time of 2:03:59 when he won the 2008 Berlin marathon, hurt both knees in a fall during practice.
Gebrselassie announced his retirement from the sport in November last year, only to reverse the decision days later.
He has said a knee injury and his failure to finish the New York marathon earlier in the month were the reasons for his unexpected — and short-lived — retirement.
Sunday’s Tokyo marathon would have been his first race since the New York outing.
Big names from the world of marathon running set to compete this weekend include Felix Limo of Kenya, who set his personal best of 2:06:14 winning the 2004 Rotterdam marathon, and Yemane Tsegay of Ethiopia, whose personal best of 2:06:30 was only enough to bag a fourth place in the 2009 Paris marathon.
Kenya’s Paul Biwott and Salim Kipsang are also expected to pose a threat with their best times of 2:07:02 and 2:07:29, respectively, while Ethiopia’s Hailu Mekonnen has a best time of 2:07:37.
Other major athletes will be Tadesse Abraham of Eritrea and last year’s Hokkaido marathon winner Cyrus Gichobi Njui of Kenya, while representing Japanese hopes will be Masakazu Fujiwara, Arata Fujiwara and Satoshi Irifune.