Her absence comes after Buckingham Palace announced the Queen would miss the annual Remembrance Sunday service at the Cenotaph in London because she has sprained her back.
Prince Edward, the Queen’s youngest son, told the assembly that the Queen sends her “sincere and deep apologies” that she could not attend.
“I think you probably understand why, and she regrets that deeply,” he said before delivering a speech on her behalf.
In her address, the Queen said the church had brought hope during the pandemic.
“Of course, in our richly diverse modern society, the well-being of the nation depends on the contribution of people of all faiths, and of none,” the royal said.
“But for people of faith, the last few years have been particularly hard, with unprecedented restrictions in accessing the comfort and reassurance of public worship.”
During the first two national lockdowns, places of worships were ordered to close across England.
The Queen added: “For many, it has been a time of anxiety, of grief, and of weariness. Yet the Gospel has brought hope, as it has done throughout the ages; and the Church has adapted and continued its ministry, often in new ways, such as digital forms of worship.”
The event marks the first time the monarch, who is the supreme governor of the church, has missed a visit to the Synod in its 51-year history.
The full assembly, which usually meets two or three times a year, had not been able to meet in person since before the pandemic in February 2020.
During the 11th session, members will discuss pressing national issues such as the economic gap between the rich and the poor.
In her address, the Queen also noted the absence of her late husband, Prince Philip, who died in April.
“It is hard to believe that it is over 50 years since Prince Philip and I attended the very first meeting of the General Synod,” she said.
“None of us can slow the passage of time; and while we often focus on all that has changed in the intervening years, much remains unchanged, including the Gospel of Christ and his teachings.”
Concern for the Queen’s health has risen in recent weeks, after she spent a night in hospital in October.
At the time, Buckingham Palace said she had been admitted to undergo “preliminary checks”.
Following the stay, she has cancelled a number of scheduled appearances such as at Cop26 and a visit to Northern Ireland.
Additional reporting by PA
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