Minister for Foreign Affairs Julie Bishop joined the launch of the embassy via live video streaming, in recognition of Estonia’s most successful start-up, Skype.
The Embassy will be a temporary presence for 12 months.
Minister Bishop confirmed an Australian Defence Force member will be seconded for a three-moth period each to year to the NATO CCDCOE, a multinational and interdisciplinary hub of cyber defence expertise.
"Australia welcomes the opportunity to deepen engagement with the world-leading cyber defence experts at the NATO CCDCOE," the minister said in a statement.
"Now, more than ever, we must engage with the international community to set clear expectations for responsible state behaviour in cyberspace. The international rules based order applies online, just as it does offline."
Australia will also observe this year’s CCDCOE-run annual cyber defence exercise, Locked Shields.
The 2017 exercise saw participants defend networks in the face of severe simulated cyber attacks on the electricity grid, drones, military systems, and critical IT infrastructure.
Sponsoring nations include key NATO members as well as Austria, Finland, Sweden and Australia. Australia is the second non-NATO country outside the EU to join the organisation. Japan joined the NATO CCDCOE in January.