But the church's call has angered many of the friends and relatives of those kidnapped and killed under military rule.
'Turning its back'
Outside the presidential palace in Santiago, Chile's capital, hundreds of people held photographs of dead or missing relatives.
"We're not seeking to reopen the wounds of the past, nor close them completely"
president of the Episcopal Conference
"We've heard Monsignor [Alejandro] Goic [president of the Episcopal Conference] say that nobody would be left out of this proposal. That means it includes human rights abusers, and that's unacceptable," Lorena Pizarro, the president of the Relatives of Missing Detainees Association, said.
The church "is turning its back on the victims [of the dictatorship]. When you speak of mercy you have to see both sides of the coin. There are many older ladies here who are still waiting to know what happened to their loved ones".
The group says about 35 military personnel jailed for crimes during the so-called "dirty war'' would apparently would be eligible for pardon, although officials have not given an exact number.
According to official statistics, 3,065 opponents of Pinochet's government were killed and 1,200 more disappeared during its 17-year rule.
About 600 military personnel have been accused of crimes against humanity but no more than 150 are now in prison.
Pinochet, a controversial figure who is still admired by some but hated by many, died in 2006 without ever being convicted on charges of human right abuses.
The church's proposed amnesty would apply to prisoners who are sick, older than 70 or those who have served half their sentence. It could mean immediate release or reduced sentences.
The main opposition to the pardons comes from the centre-left, which has a majority in congress, but some members of Pinera's conservative bloc are also uneasy at the idea of seeming to go easy on convicts.
Pinera, who has sought to distance his brand of conservative politics from the far-right Pinochet dictatorship, is said to be considering the proposal.
Church officials said officers convicted of rights abuses were included in an effort to trigger national debate.
"We're not seeking to reopen the wounds of the past, nor close them completely," Goic said.
"We're simply showing authorities the pain of those deprived of their freedom, who have been tried and have served most of their sentences."