The Eagles say Secondary coach Sean McDermott will coach the defense in the interim.
"Jim and I agreed that he needs to concentrate all of his efforts on his recovery," said head coach Andy Reid in a statement. "His health is number one. He's struggling, but he's a tough guy and a true battler. I hope everyone will keep him in their thoughts and prayers during this period of time. We hope to have him back with the team as soon as possible."
Johnson, who turns 68 on May 26, first was diagnosed with cancer in 2001. The team disclosed the recurrence in January, nearly two weeks after it lost to the Arizona Cardinals in the NFC Championship.
Because of the pain in his lower back, Johnson coached that game and the victory over the New York Giants in the division playoffs a week earlier from the press box.
Earlier this month, Johnson told reporters at the Eagles first minicamp that he was feeling fine, though he had to use a cart to get around the fields.
The Associated Press contributed to this report.
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