The bill is in response to an incident last year in which the Estlink 2 electricity cable and four telecom cables linking Finland and Estonia that lie on the Baltic seafloor were damaged.
Investigators suspect the cables were damaged by the anchor of the Eagle S, a Cook Island-flagged oil tanker believed to be part of a so-called "shadow fleet" used to export Russian oil.
"There's a point to every law. In this case, the reason for it is our eastern neighbour who poses a real danger to us," Estonian national security committee chairman Meelis Kiili said in parliament on Wednesday, referring to Russia.
Tensions have mounted around the Baltic Sea since Russia's invasion of Ukraine in February 2022.
Experts and politicians have said recent actions targeting vital infrastructure are part of a hybrid war between Russia and Western countries.
Estonia, a small EU and NATO member, has been a staunch supporter of Ukraine since the invasion.
The Estonian bill still needs to be signed by the president and published in the public journal to take effect.
It was approved unanimously by the 62 out of 70 lawmakers present for the vote.
"The security environment around us and on the Baltic sea, which has through the ages been one of the most peaceful naval environments, is unfortunately getting worse," said lawmaker Peeter Tali.
The bill's explanatory note said that to date the defence forces were mainly allowed to use force to defend Estonia's border, repel attacks on Estonian territory and intervene if the life of a civilian were in danger.
It said the government initiated the bill to strengthen maritime security, allowing the defence forces to intervene in the event of danger posed by a civilian ship.
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