The Earl of Wessex will deliver the Queen's address to the General Synod on her behalf on Tuesday as he represents his mother at the Church of England's national assembly.
The Queen who missed the Remembrance Sunday service at the weekend, was due to appear in person at the Synod, but her appearance was cancelled last week.
She has now been under doctors' orders to rest for nearly a month after spending a night in hospital on October 20 undergoing preliminary investigations, and is at Windsor Castle and only undertaking light duties.
Edward will read the 95-year-old head of state's speech to bishops and clergy at Church House, the Westminster headquarters of the Church of England.
The Queen's youngest son will also inaugurate the Synod on the Queen's behalf, and attend a service at Westminster Abbey beforehand.
The General Synod's Notice Paper on the Church of England website said the ceremony would consist of a speech by the Archbishop of Canterbury greeting the earl, a formal announcement of Returns by the Registrar and the Secretary General, followed by a short address delivered on behalf of the Queen and a response by the Archbishop of York.
It is the first time in the Synod's 51-year history that the monarch 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.
In 1970, the year the Synod replaced the Church Assembly, Elizabeth II became the first sovereign to inaugurate and address the gathering in person.
Since then she has inaugurated and addressed the opening session every five years after diocesan elections.
The 2020 elections were postponed to this year due to the pandemic.
There are 483 members of General Synod. Members are arranged into three Houses, bishops, clergy and laity, with the latter made up of lay members.
The Synod considers and approves legislation affecting the whole of the Church of England, formulates new forms of worship, debates matters of national and international importance, and approves the annual budget for the work of the church at national level.
The Queen pulled out the national Remembrance Sunday service at the weekend after spraining her back, Buckingham Palace said.
She is due to carry out virtual audiences later this week, but has no major public engagements planned for the rest of the year.
Concern for her health has increased given her age and due to the number of major engagements she has missed in recent weeks.
She cancelled a two-day trip to Northern Ireland, and pulled out of attending the Cop26 climate change summit, the Festival of Remembrance, Remembrance Sunday and the Synod.
The Queen's husband the Duke of Edinburgh died in April age 99.
Saturday marks their first wedding anniversary to pass since Philip died.
The Queen and the duke would have celebrated 74 years of marriage.
Register now for one of the Evening Standard's newsletters. From a daily news briefing to Homes & Property insights, plus lifestyle, going out, offers and more. For the best stories in your inbox, click here.