Ali died last Friday at the age of 74 in hospital in Phoenix, Arizona.
World leaders will be among thousands attending Friday's procession and memorial service in Louisville, Kentucky, where Ali was born.
The White House said Mr Obama and his wife Michelle will be at daughter Malia's high school graduation.
They will send a letter to the Ali family with White House senior adviser Valerie Jarrett, who knew Ali.
Bob Gunnell, a spokesman for the Ali family, said Mr Obama and Ali's widow Lonnie had spoken by telephone.