The Duke of Edinburgh is one of the last people to be awarded a knighthood by Australia after the country scrapped the title, describing it as inappropriate in the modern honours system.
Philip was knighted by the Queen in Windsor Castle earlier this year, having been granted the Knight of the Order of Australia award by Australia's then prime minister Tony Abbott.
The Queen has now agreed to a recommendation to remove the titles of knights and dames from the Order of Australia, Prime Minister Malcolm Turnbull said.
The country's cabinet agreed "knights and dames are not appropriate in our modern honours system," Mr Turnbull, a republican who replaced Mr Abbott in September, said.
The announcement on Australia Day in January that Philip was to receive a knighthood was widely criticised at the time, with some suggesting it sounded like a joke.
Philip's knighthood from Australia, a title he will retain, is one in a long list of accolades he has been awarded over the years.
He is already a Knight of the Order of the Elephant in Denmark, a Royal Chief of the Order of Logohu in Papua New Guinea, and a Knight Grand Cross of the Order of the Netherlands Lion.
Mr Abbott said at the time the award was for a long life of duty and service, citing Prince Philip's Duke of Edinburgh award scheme as having helped thousands of young people in Australia for more than 50 years.
But members of the public said giving a member of Britain's royal family the country's highest honour had created a "time warp".
Australia previously scrapped the honorary titles in 1986 but they were reinstated by Mr Abbott last year.