A spokeswoman for the president said, Obama and his wife Michelle will be in Washington for their daughter Malia’s high school graduation ceremony.
The Obamas, however, are sending a letter to be read at Friday’s service in Louisville, Kentucky.
Meanwhile, Ali’s widow, Lonnie spoke to Obama over the phone and appreciated his kind words and condolences.
Ali’s family spokesman announced Turkish President Recep Tayyip Erdogan and King Abdullah II of Jordan will also no longer address the congregation, but they are expected to attend the service.
Former world heavyweight boxing champion Lennox Lewis and Hollywood star Will Smith – who portrayed Ali in a 2001 film about Ali’s life – will be among the pallbearers.
Some 15,000 people are expected to attend the funeral of Muhammad Ali at the KFC Yum! Centre followed by a procession through the streets of the boxer’s hometown.
The three-time world heavyweight champion died in Phoenix, Arizona, last Friday at the age of 74. With Parkinson’s disease for 32 years, Ali underwent a treatment earlier in the week at a hospital with a respiratory condition. The cause of his death was a septic shock due to unspecified natural causes, his family said.