The former Great British Bake Off winner is part of the show's first all-male couple with professional dancer Johannes Radebe and the couple topped the leaderboard last week with their score of 39/40 for their Argentine Tango.
But Whaite revealed on Instagram on Tuesday: "Going home to rest. My hip flexors are in so much pain and the physio has recommended a day of rest.
"I'll watch Christmas films all day and eat Haribo."
Watch: Who is Strictly's John Whaite?
However the rest paid off as the 32-year-old baker revealed that he had slept for 13 hours and said: "I feel like a new man today and my hips are ready to shake like Shakira."
This week the pair — who are yet to score a perfect 40 from the judges — will be dancing a Salsa to We Are Family by Sister Sledge.
Last week saw Tilly Ramsay became the latest celebrity to be sent home by the judges.
CBBC presenter Rhys Stephenson landed in the dance-off following the public vote, despite being placed third by the judges' score for his Viennese Waltz, which saw him break down in tears on the dancefloor.
Walker revealed he has received abusive messages from angry viewers who do not believe he deserves to still be in the competition.
The 44-year-old TV presenter tried to laugh off the online abuse he had received as he shared it on Twitter.
He said: "Thank you to everyone who is sending lovely messages & enjoying us having fun on #Strictly and to the few who say… “Just leave” “Aren’t you ashamed?” “You’re a disgrace” “It’s a fix” (which I don’t get) or “Who is voting for them?” IT’S A TV SHOW! See you in the 1/4 finals."
Watch: John Whaite said his Strictly dance partner has changed his life