A former Chilean bishop staunchly defended by Pope Francis after being accused of helping to conceal sexual abuse has been named a suspect in two criminal investigations into alleged cover-ups, a prosecutor and another legal source said on Friday.

Juan Barros, whose resignation as bishop of Osorno was accepted by the Pope in June alongside those of four other bishops, was interrogated as a suspect for more than three hours on Thursday in Santiago, city prosecutor Raul Guzman said.

Separately, prosecutor Emiliano Arias has named Barros as a suspect in the cover-up of several sex abuse cases in Rancagua, a city just south of the Chilean capital, the legal source told Reuters on condition of anonymity.

Barros is due to be questioned over the cases shortly, the source said. The cases have not yet been identified.

Barros was accused of protecting Rev Fernando Karadima, his former mentor who was found guilty by a Vatican investigation in 2011 of abusing teenage boys over many years. Barros has maintained he was unaware of any wrongdoing.

In January, the pope was forced to apologise after dismissing allegations against Barros as 'slander' and 'without evidence' during a visit to Chile.

Barros told journalists after being questioned by the Santiago police's Sexual Crimes Unit on Thursday that he was a suspect in the cover-up of the case of Father Pedro Quiroz, a former military chaplain who fell under his direction when he was the country's military bishop between 2004 and 2015.

'I contributed what I could contribute. I told the prosecutor what I knew or didn't know,' Barros said.

Speaking to journalists after the interrogation, Guzman confirmed that Barros was a suspect in the Quiroz case.

According to a statement posted on the military bishopric's website, a complaint of abuse in 1997 was filed against Quiroz in July 2018. The priest was previously investigated by the Vatican over abuse allegations in 2000, but the case was shelved for lack of statements from the alleged victims, the statement said.

The office of the bishop to the armed services in August became the latest in a series of Church facilities raided by Chilean prosecutors who have launched one of the world's most aggressive investigations into the abuse scandal.

Arias, the prosecutor, seized documents related to complaints made over 20 years to Santiago Silva, the current military bishop, and his predecessor, Barros, of clerical sexual abuse inside and outside the armed forces.