The Earl of Wessex delivered the Queen's address to the General Synod on her behalf on Tuesday, as Her Majesty continued to rest at Windsor Castle.
Prince Edward represented his mother at the Church of England's national assembly at Church House in Westminster. The monarch, 95, had been due to attend the event in person.
It is the first time in the Synod's 51-year history that the Queen has not made her five-yearly visit to coincide with diocesan elections. She is the Supreme Governor of the Church of England and has a deep Christian faith.
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The Earl told the General Synod "you probably understand why" the Queen was not present to deliver her address.
Edward said the monarch sends her "sincere and deep apologies that she cannot be here today".
He added: "I think you probably understand why, and she regrets that deeply."
© Photo: Getty ImagesThe Earl delivered an address on behalf of the Queen
The Earl delivered the Queen's message, which read: "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. 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.
"The list of tasks facing that first General Synod may sound familiar to many of you: Christian education; Christian unity; the better distribution of the ordained ministry to the needs of the population. But one stands out supreme: 'to bring the people of this country to the knowledge and the love of God'.
"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."
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© Photo: Getty ImagesEdward also attended a service at Westminster Abbey
It comes after the Queen pulled out of the Remembrance Sunday service last-minute after spraining her back, Buckingham Palace said.
She has now been under doctors' orders to rest for nearly a month after spending a night in hospital on 20 October undergoing preliminary investigations, and is at Windsor Castle and only undertaking light duties.
Her Majesty is due to carry out virtual audiences later this week, but has no major public engagements planned for the rest of the year.
As well as pulling out of attending the Synod and Remembrance week events, the Queen also cancelled a two-day trip to Northern Ireland last month, as well as an appearance at the COP26 climate change summit in Glasgow.
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