The move was criticised by the British Medical Association, which represents more than 140,000 doctors and medical students.
A BMA spokesman said the sport should "play no part in a modern Olympic games".
He added: "Irrespective of their gender, during the course of a fight boxers can suffer acute brain haemorrhage and serious damage to their eyes, ears and nose.
"Throughout their career, boxers will receive thousands of blows to the head. Each blow received results in the brain being shaken within the skull.
"The cumulative affect of a lifetime in the ring can be irreversible brain damage. Unlike other sports the aim of boxing is to inflict bodily harm on an opponent."
Former boxer and Labour MP Paul Flynn described the decision as "foolish" and said it was not a step forward for female equality.
The politician, who has tabled two private members' bills to get boxing banned, said: "This is a foolish act. I'm very disappointed to see it's being presented as something to do with women's rights."
He added: "If anyone still believes boxing is a healthy sport there's two words for them - Muhammad Ali."
British boxer Amir Khan, an Olympic silver medallist in 2004, said: "Deep down I think women shouldn't fight. That's my opinion.
"When you get hit it's very painful. Women can get knocked out."
However, he told BBC Radio 5 live: "I am going to be supportive. I'll be cheering on the British fighters and hoping they win the medals."
Although the head is not a target zone in amateur boxing, one organisation expressed concern at further promoting the sport of boxing as a whole.
Peter McCabe, chief executive of brain injury association Headway, said: "We believe all forms of boxing should be banned with immediate effect.
I have seen at first hand the massive improvements that have taken place in competitive women's amateur boxing over the last few years,
Richie Woodhall Former world boxing champion
"Introducing women's boxing at the Olympics will simply serve to glamorise a dangerous and irresponsible sport to a new audience and lead to more young women putting their health at risk."
Khan admitted he had never seen a women's fight, whereas former WBC super-middleweight world champion Richie Woodhall, now a coaching consultant to the British Amateur Boxing Association, says the change is deserved.
"I have seen at first hand the massive improvements that have taken place in competitive women's amateur boxing over the last few years," he said.
Sue Tibballs, chief executive of the Women's Sport and Fitness Foundation, welcomed the shift towards equality at the Olympics.
"In Beijing, 165 medals were available to men versus 127 to women," she said. "Women were first allowed to compete in the Olympic stadium in 1922 - 90 years on, we hope London 2012 will show real progress for sportswomen."
In all, 17 sports submitted applications for changes to their programmes. Among them:
Canoe sprint - all men's 500m events will be shortened to 200m to make them "more spectacular"; men's canoe double 500m to be replaced by women's kayak single (K1) 200m.
Handball - all placement matches below the bronze-medal play-off will be removed.
Modern pentathlon - the new combined run/shoot format has been included.
Tennis - a mixed doubles event will be included, subject to confirmation from the International Tennis Federation that top singles players will take part.
Wrestling, Swimming, Cycling - all want new events, which will be allowed only if they replace current events and do not increase the number of athletes.
Sailing - Tornado Multihull event withdrawn, reducing the programme to 10 events.
Final decisions on details will be made at the IOC executive board's December meeting in Lausanne.
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