The 30-year-old Briton, who is also the world champion, is "really frustrated" but wants to be "100% ready" to defend her Olympic title in Rio in August.
The indoor season begins in Glasgow on 20 February.
"My priority has always been Rio and I don't want to take any risks in the short term," said Ennis-Hill.
"I am understandably frustrated but know this is the right approach."
Ennis-Hill struggled with an Achilles problem in 2013 and missed the World Championships in Moscow that year.
She also missed the entire 2014 season as she gave birth to her son.
Ennis-Hill returned to training in the autumn of that year and went on to win heptathlon gold at the 2015 World Championships in Beijing.
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Olympic heptathlon champion Jessica Ennis-Hill will miss this year's indoor athletics season because of an Achilles injury.