The navy stressed that there was no danger to critical infrastructure. Previous incidents had seen underwater cables damaged in suspected sabotage.
Security analysts say Russia is operating a large "shadow fleet" of hundreds of vessels, seeking to dodge the sanctions Western nations imposed on its oil exports over the war in Ukraine.
Several undersea Baltic cables were damaged last year, with many experts calling it part of a "hybrid war" carried out by Russia against Western countries.
"The purpose of detaining the ship was to check its papers and legal status," Estonian navy commander Ivo Vark told reporters.
"The detention and the investigations carried out are in no way related to damage to critical infrastructure," he added.
The vessel, the Kiwala, is under sanctions from Canada, the European Union, Switzerland and the United Kingdom and was on its way to the Russian port of Ust-Luga, according to Vark.
The navy said its inspection found the Kiwala to be stateless. A certificate saying it sailed under the flag of Djibouti was disputed by the African country, it added.
"It's no secret that during this last year enough vessels without papers have appeared in the Gulf of Finland," Estonian border guard head Veiko Kommusaar said.
"And it's safe to say this is part of the shadow fleet," he added.
Kommusaar said the captain was Chinese, with most of the 24-member crew from either China or Mauritania.
Estonia's leading Postimees daily reported that the tanker is owned by Tirad Shipping Inc, which has just this one ship and is registered in Mauritius.
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