The agency said a fourth internet cable running between Finland and Germany and belonging to the Finnish group Cinia was also believed to have been severed.
Both the Finnish and the Estonian governments will hold extraordinary meetings later on Thursday to assess the situation, they said in separate statements.
Baltic Sea nations are on high alert for potential acts of sabotage following a string of outages of power cables, telecom links and gas pipelines since 2022, although subsea equipment is also subject to technical malfunction and accidents.
The European Union said it strongly condemned any deliberate destruction of the continent’s infrastructure.
“We commend the Finnish authorities for their swift action in boarding the suspected vessel,” said a joint statement from EU foreign policy chief Kaja Kallas and the European Commission, the bloc’s executive body.
Repairing the 170km Estlink 2 interconnector will take months, and the outage raised the risk of a strained power supply during the winter, operator Fingrid said in a statement.