Tax and Customs Board officials said they destroyed a grow with 69 plants discovered in Põlva County in the southeast of the country, part of an increasing trend.
Three Estonian citizens were apprehended in the raid in the first week of June.
Public Prosecutor Taavi Pern said such operations are discovered around three or four times a year, and said the estimated proceeds on the black market could have run up to over 20,000 euros.
Tax and Customs Board drug interdiction director Urmet Tambre said the seizure was a sign of stepped up efforts to fight narcotics and psychotropics at airports, ports and the nation's roads.
The officials said they were keeping an eye on the mail due to orders of cannabis seeds. "The orders for pot seeds increase every spring. If we have probable cause to believe that they are for illegal pot cultivation, the people who ordered them can be sure that they will be subject to our scrutiny," said Tambre.
The latest airport bust also occurred in early June and saw two Dutch citizens found in possession of 53 kg of khat, a mild euphoric and stimulant similar to coffee, used in East Africa and parts of the Arabian peninsula.
While khat has long been legal in Britain, this shipment came in through Amsterdam. Estonian authorities have taken a dim view of the substance, with a Somalian who was transporting khat to Finland, reportedly for a wedding gathering, receiving a long prison term.