The Queen also missed the Christmas Day service at her Norfolk estate and has not been seen in public for 12 days.
Meanwhile, a Buckingham Palace spokeswoman said the Queen was “still recuperating”.
Queen Elizabeth and Prince Philip left for their Christmas break a day late on December 22, travelling by helicopter instead of train, because of colds. The Duke of Edinburgh has made a full recovery.
When she arrived at the church, Princess Anne was asked how her mother was, to which she replied “better”.
Princess Anne attended the New Year’s Day service alongside her father, Prince Philip, and her brother, Prince Edward, as well as other members of the Royal Family.
Queen Elizabeth’s absence from church on Christmas Day was the first time she had missed the service in many years.
According to the Buckingham Palace, that was a “precautionary measure” in the cold and wet conditions and it had “no sense of undue concern”.
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