Campaign groups have long accused President Teodoro Obiang Nguema Mbasogo's government of arbitrary detentions and torture during his four decades in power in Spain's former colony in central Africa.
The Spanish High Court is investigating one of Obiang's sons, Carmelo Ovono Obiang, his security director Isaac Nguema Endo and Security Minister Nicolas Obama Nchama, the source said.
The trio are suspected of having kidnapped and tortured two Spanish nationals who oppose Obiang's government and were arrested in South Sudan in 2020 and flown to Equatorial Guinea.
Two other dissidents, Equatorial Guinea nationals who reside in Spain, were kidnapped at the same time, said the source, who confirmed a report in the Spanish national daily El Pais. The interior ministry declined to comment.
The court, which handles major criminal cases, opened its probe after receiving a complaint from relatives of the victims.
Under Spanish law, courts sit in judgement on cases and can launch investigations into alleged crimes, and refer the case for trial if there is enough evidence.
El Pais said the opponents arrested in South Sudan were flown to Equatorial Guinea aboard a "presidential plane."
According to police reports seen by the newspaper, the three Guinean officials under investigation by the court "repeatedly participated in torture sessions" to extract confessions from the four.
The four were hung by their feet causing their "blood vessels to explode", received electrical shocks and had boiling water thrown on their naked bodies, it said.
On the basis of these confessions, they received jail terms of between 60 and 90 years for allegedly taking part in an attempted coup against Obiang.
The accusations against the three officials is based on testimony from two protected witnesses and from some of the alleged victims, according to El Pais.
Aged 80, Obiang is the world's longest-serving president. He has ruled Equatorial Guinea since taking power in a coup in 1979, 11 years after independence from Spain.
Political dissent has been suppressed and the country's oil wealth benefits an elite few, watchdogs say.
In November, Obiang was re-elected to a sixth term with 94.9 percent of the votes cast in an election that saw a turnout of 98 percent, according to official figures.