The 2010 series was a follow-up from the original 1971-1975 series she created with fellow actress Jean Marsh, and although she did not appear in the original, she has played a featured role in the new version.
"It's with much sadness that we say goodbye to her wonderful character, the straight speaking mother-in-law Lady Holland," the BBC said in a statement Sunday.
"However, we respect her decision and we will be announcing new star casting soon."
Atkins reportedly has been unhappy with the direction the show is being taken in with its new scripts.
The new version features the fortunes of a diplomat's family and their servants upstairs and downstairs in a large London townhouse, with six new episodes set for filming in October for broadcast in 2012.