President Teodoro Obiang Nguema seized power in the oil-rich former Spanish colony in 1979 and has faced a string of coup attempts during nearly four decades in office.
Critics accuse him of brutal repression of opponents as well as election fraud and corruption.
“The restrictions on freedom and arrests, particularly those of political opponents … since the elections in November 2017 arouse grave concern,” said Catherine Ray, EU spokeswoman for foreign affairs and security policy, in a statement.
“The death in custody of Mr Ebee Ela, a member of the opposition party Ciudadanos por la Innovacion (CI, Citizens for Innovation), confirms the sharp decline in the human rights situation,” Ray said.
Santiago Ebee Ela, 41, who was detained on January 2, died at the police headquarters in the capital Malabo of “cruel torture”, the CI party has said.
President Nguema said Ebee Ela was “sick” and that the death was not due to ill-treatment and promised an investigation.
“Competent authorities in Equatorial Guinea should investigate in appropriate fashion without delay to clarify the reasons for the death,” the EU’s Ray responded.
On January 3, Malabo announced that security forces had foiled an attempted coup on December 24, after the arrest of about 30 foreign armed men just inside Cameroon at the junction with Gabonese and Equatorial Guinean territory.
The EU said the trials should be fair and in line with international norms.
From the mid-1990s, Equatorial Guinea became one of sub-Saharan Africa’s biggest oil producers, but about two-thirds of its 1.2 million people live below the poverty line.