Britain's Queen Elizabeth II on Monday signed a charter calling for an end to discrimination across the 54 Commonwealth nations after earlier missing a function as she recovers from the symptoms of gastroenteritis.

She called the agreement "a significant milestone" for the organisation.

"We now have a single document that captures the core values of the Commonwealth and all its members," she said at a London reception to celebrate Commonwealth Day.

"I hope the carefully chosen words of the charter will reinvigorate efforts already begun to make the Commonwealth fit and agile for the years ahead."

The 86-year-old monarch earlier missed a Commonwealth Day service as she recuperates from the illness that hospitalised her for the first time in 10 years last week.

She was discharged last Monday after an overnight stay in a private London hospital.

The monarch, who is the head of the 54-member Commonwealth of Nations, was "regrettably" unable to attend the service at Westminster Abbey, "as she continues to recover following her recent illness," the palace said in a statement.

Her 91-year-old husband Prince Philip represented her at the service, which was attended by Commonwealth ambassadors, or high commissioners, from around the world and featured an address from Virgin tycoon Richard Branson.

"This time last week she was in hospital but she's in great spirits and apart from this is in good health," a Buckingham Palace spokeswoman said.

"It's just the tail end of the symptoms, her condition has not worsened at all."

At the evening reception at the organisation's Marlborough House headquarters, the queen signed the new Commonwealth charter, a document that includes commitments to gay rights among other issues.

She also hopes to undertake some other official engagements planned later this week, Buckingham Palace added.

The BBC, Britain's publicly-funded national broadcaster, reported that doctors had recommended it would be best for the queen not to sit through an hour-long church service.

It is the first time the queen has missed a Commonwealth Day Observance service for 20 years, the last occasion being when she had flu in 1993.

Last week the queen had to cancel a visit to Rome and other engagements after she was hospitalised with the stomach bug.

The queen celebrated her diamond jubilee marking 60 years on the throne last year and has been known for enjoying robust health and rarely missing engagements.

The 16-point charter being signed by the Commonwealth later Monday was adopted in December by all nations in the group. It aims to protect democracy, the rule of law, international security and free speech.

"We are implacably opposed to all forms of discrimination, whether rooted in gender, race, colour, creed, political belief or other grounds," the document reads.

Gay rights group Stonewall said it was the "first time that the queen has publicly acknowledged the importance of the six percent of her subjects who are gay."

But Australian-born gay rights campaigner Peter Tatchell said the sovereign had made no "explicit commitment" to homosexual equality.

Queen Elizabeth is head of state of 16 Commonwealth realms including the United Kingdom, Canada, Australia and New Zealand.

Her titles also include head of the Commonwealth, which mainly groups territories of the former British empire.

The queen is due to attend the bi-annual Commonwealth heads of government summit in the Sri Lankan capital Colombo in November. She has been present at every summit since 1973.

Prince Philip once described the queen as the "Commonwealth psychotherapist" due to her informal talks with government leaders at the summits.

The Duke of Edinburgh has himself suffered from health problems in recent years.

He had to spend Christmas in 2011 in hospital after being rushed for surgery on a blocked coronary artery.

Prince Philip was hospitalised again in June 2012 with a urinary tract infection that caused him to miss part of the diamond jubilee celebrations.