Marler said he needs to rest following a gruelling season which ended with bans following two high-profile transgressions.
"Whenever you play for England you have to be 100 per cent and unfortunately I'm not in that place at the moment," the 25-year-old said in a statement on the RFU website.
"It's not a decision I've come to lightly, but I feel I would be letting my team mates and my country down if I were to tour.
"I think a short rest will really help me recharge my batteries so I can start next season with the energy and focus that’s needed to perform at the highest level."
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England coach Eddie Jones Marler would be a big loss.
"We fully support Joe's difficult decision and admire his honesty," the Australian said.
Marler recently revealed he was seeing a sports psychologist to address his "lack of professional control" following bans for calling Wales forward Samson Lee "gypsy boy" during a Six Nations game and kicking an opponent in the head in a Challenge Cup match.
England play Wales at Twickenham on May 29. The test series against Australia starts in Brisbane on June 11.
(Reporting by Neil Robinson, editing by Ed Osmond)
