The blonde dancer injured herself in training for the BBC One dance competition ahead of this weekend's launch.
Natalie told The Sun not being part of the show would be "hard" but added: "This series is going to blow everyone away and I cannot wait to get my feet back on the dance floor."
Natalie was partenered with England cricketer Michael Vaughan in the last series of SCD, finishing in seventh place.
A BBC spokesperson said Natalie would return to the show "as soon as she is fit to".
In the meantime, the star will be replaced by fellow pro dancer Aliona Vilani, who tweeted last night: "Can speak about it now OFFICIALLY: I'm doing Strictly Come Dancing 2013 and I'll be on your tvs full time doing my thing Vilani style."
She added this morning: " I'll be replacing injured Natalie to pair up with a celeb in the new Strictly series and dance with Brendan in pro numbers."
Aliona is no stranger to injury. She was due to perform on last year's Strictly with Johnny Ball, but had to pull out after an injury in rehearsals.
So far, four celebrities have been confirmed for the new series of SCD: Vanessa Feltz, Susanna Reid, Abbey Clancy and Rachel Riley.
Watch the first trailer for Strictly's new series below: