"The country has made remarkable progress in transforming its energy sector, and there is every reason to expect that this successful process will continue and be reinforced through IEA membership," she said in a statement.
To become a full member, Estonia was required to set aside enough oil stocks to satisfy the equivalent of 90 days worth of imports from 2013.
Estonian Minister of Economic Affairs Urve Palo said accession is a milestone for the Baltic nation.
Estonia, Van der Hoeven said, is welcomed to the IEA as a member country that prioritizes energy security and economic sustainability.
The International Monetary Fund said in its latest assessment the Estonian economy was doing well, but there may be issues with high levels of unemployment in the country.
The fund said the economies of Baltic countries in general are struggling with higher energy costs. While some have secured alternative energy options, "all countries could do more."
Estonia's membership was endorsed by IEA members in November.
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