Earlier, the monarch and her husband, the Duke of Edinburgh, planted two eucalyptus trees in the lawns of Government House in Canberra.
Wearing an apricot dress with leaf designs, the Queen and Prince Philip also met the families of staff who work at the Governor-General's residence.
Treasurer Peter Costello also presented the royals with a special set of Mint coins.
Duke questions GM appropriateness
During his tour of Australia's national science headquarters in Canberra, Prince Philip questioned the development of genetically modified plants, a key plank of CSIRO's research.
He says farmers need to know what the alternatives are.
Duke questions GM plants
Meanwhile, Prince Charles has led the Commonwealth Day celebrations in Britain, taking part in a colourful ceremony in central London.
Accompanied by his wife Camilla, the Duchess of Cornwall, Prince Charles read out Queen Elizabeth's Commonwealth Day message to a 2,000-strong multi-faith congregation at Westminster Abbey.
The Queen, as head of the Commonwealth, is in Australia to open the Commonwealth Games in Melbourne on Wednesday.