Estonia has had an embassy in Canberra since 18 February 2015, which is also responsible for relations with New Zealand, Fiji, Tonga, Samoa, Vanuatu and PNG, and also has Honorary Consulates in every state capital.

[4] Following the Estonian Declaration of Independence in 1918, from 1919 to 1935, Estonia was represented in Australia by the Finnish Consulate in Sydney, another country that had emerged from the dissolution of the Russian Empire.

Formal relations between the two countries began when Australia recognised Estonia on its admission to the League of Nations on 22 September 1921.

[5] In 1935 Estonia appointed its own honorary consul, Johannes Kaiv, who served until his promotion to Consul-General in New York in 1939.

[12] With the Soviet Occupation of the Baltic States in June 1940, the Australian Government of Robert Menzies, like the British Government, did not recognise this action but the Minister for External Affairs, Sir Frederick Stewart, later confirmed in June 1941 that informal discussions had occurred that implied a "readiness on the part of the United Kingdom Government to settle on a practical basis various questions arising out of the Soviet annexation of the Baltic States.

By March 1949, in a Senate debate on the United Nations General Assembly's Third Session, the Minister for Health and Social Services, Senator Nick McKenna, noted the status quo of the situation:[15] "The Australian Government has not recognized, and does not intend to recognize, the absorption into the Soviet Union of the formerly independent republics of Latvia, Lithuania, and Estonia.

The Australian Government believes that these accessions by the Soviet Union cannot be said to have been made as a result of the clearly expressed wish of the people of those countries.

"[16] Australia was the only Western country to break ranks and briefly recognise the Soviet annexation of Estonia (and the other Baltic states) as de jure for 17 months between July 1974 to December 1975 by the Whitlam Labor government, while most other countries continued to recognise the independent Estonian diplomatic missions.

It was something which took place as a result of a disgraceful, shameful and discreditable treaty signed in Moscow in 1939 between Stalin and Ribbentrop, the then nazi Foreign Minister.

[20] On 27 August 1991, Prime Minister Bob Hawke, announced Australia's decision to re-establish full diplomatic relations with Estonia.

[27] In November 2011, the Ministry of Foreign Affairs opened a Consulate-General in Sydney, headed by Consul-General Triinu Rajasalu.

[1] Estonian Parliamentary delegation, led by the Speaker of Riigikogu Ene Ergma visited Australia in 2008.

[33] The Embassy of Estonia in Canberra was opened in February 2015, with the first ambassador appointed, Andres Unga, who presented his credentials to Governor-General Quentin Bryce on 28 March 2013.

In response, the Estonian Foreign Minister, Sven Mikser, noted that the new embassy "will doubtlessly make Australia more prominent in Estonia and in our region on the whole".

[38] With the severe effects of the 2019–20 Australian bushfire season upon the City of Canberra, the Estonian Embassy was temporarily closed and moved to Sydney.