Bishop José Raúl Vera López of Mexico has never shied away from controversy, defending unpopular minorities ranging from illegal migrants to prostitutes.

Now, as violence between Mexican drug traffickers and security forces pushes the drug war's five-year death toll over 45,000, the Roman Catholic bishop is taking on the government. He claims that corrupt officials are allying with criminals to skim drug profits and using the military to murder criminals who might reveal any collusion.

"The use of the army was the worst mistake of [President Felipe Calderón]," Bishop Vera says in a recent interview at his diocese in Saltillo, set in the desert mountains of northern Mexico. "This strategy is covering the corrupt people in government, the people washing the money. Organized crime is growing. The destruction of the criminals is impossible if you don't put the justice of the people first."

It is a stinging rebuke from a cleric in the Catholic church, whose collective stance has been more ambiguous.

The church hierarchy initially remained largely silent on the gore that has thrust Mexico's drug war into the international spotlight.

While it is now increasingly condemning drug-gang violence and more vocally supporting Mr. Calderón's military-led strategy, the church's stance remains less clear when it comes to innocent victims of the drug-war crackdown by the military. The ambiguity is driving a wedge between priests and human rights activists within the church and the Catholic hierarchy – a divide likely to grow leading up to Pope Benedict XVI's planned visit in March.

Tensions over human rights

Roderic Ai Camp, an expert on Mexican institutions, says the church's lack of clarity comes from leaders' desire to shore up government institutions in a young democracy, even when they might be abusing their authority.

"The church is trying to pursue a fine line between condemning violence generally, while not delegitimizing the security institutions by condemning these human rights violations," says Dr. Camp, a professor at Claremont McKenna College in California.

From 2006, when Calderón began his efforts against drug trafficking, through 2010, Mexico's National Human Rights Commission has received more than 5,300 complaints of human rights abuses committed by the army.

According to a Human Rights Watch report from November, Mexican security forces may have participated in more than 170 cases of torture, as well as disappearances and extrajudicial killings.

Not speaking out for these victims could ultimately undermine the church, say some scholars.

"If the church is not providing adequate attention to the violence issues and they haven't demonstrated to people that, 'You matter as a Catholic,' I think that could be a factor [in maintaining influence]," says Joseph Palacios, a sociology professor and Catholic priest at Georgetown University.

Whereas churches elsewhere in the region have long aligned with the government, in Mexico there has been a firmer separation of church and state – though the drug war has changed that somewhat.

"There has been a coming together of the church hierarchy and government in recent years on the issue of violence," says Victor Ramos Cortes, a religion expert at the University of Guadalajara, in Mexico. He says the government has lobbied the church for support in its efforts, especially as Mexico has wearied under surging violence.

Culture wars, particularly over abortion and gay marriage in Mexico's liberal capital, have also brought the church and Calderón's conservative administration closer together.

But that closeness is causing rifts within the church, says Mr. Ramos. While the hierarchy underlines its support for Calderón, activists are demanding a change in the strategy of the drug war.

Ties between churches, traffickers?

Some churches have benefited from the criminal underworld, receiving hefty donations from members who sit in their pews on Sundays but work as traffickers during the week. Mr. Palacios says the church needs to address the local financial relationships between clergy and drug traffickers. He says priests should discourage donations from drug traffickers, not allowing them to pay for church festivals or repairs to buildings, for example.

But priests and their congregations have also been the target of violence. Masses have been interrupted by gunfire, and some priests have been shot. Many priests have reported being victims of extortion.

Despite such challenges, though, Vera has forged ahead as a priest and human rights activist. Among those he helps are the hundreds of disappeared victims of the state.

"Vera's leadership has been exceptional in helping the families of the disappeared in [the Mexican state of] Coahuila fight back fear, get organized, and find a voice," says Nik Steinberg of Human Rights Watch. "These families are demanding justice from government officials, who often find it easier to pass off victims as criminals than to conduct real investigations into their cases."

In 2010 Vera's work was recognized internationally: He was awarded the prestigious Rafto Prize in Norway, given for human rights work.

Pushback from church superiors

But outspokenness can carry a cost; Vera has faced opposition from within the church since transforming from a theological conservative to an advocate for gays and other marginalized minorities.

This summer, an anonymous group hung banners on the Saltillo cathedral criticizing Vera's theology. "We want a Catholic bishop," read one. The Vatican then summoned him to explain his support of gay rights advocates.

His words rile the government, too, but he has forged ahead nevertheless.

"There are very few men of the cloth in Mexico who speak out on any issue, left or right," says Palacios. "But Vera is also a public intellectual who has the capacity to engage non-Catholic influentials in Mexico – academics, [nongovernment organization] staff, human rights advocates, the press."

Asked about risks to his safety, Vera waves his hand: "I am inspired by the sufferings of the people," he says.

Get the Monitor Stories you care about delivered to your inbox. By signing up, you agree to our Privacy Policy

• Staff writer Sara Miller Llana contributed to this report from Mexico City.

Get daily or weekly updates from CSMonitor.com delivered to your inbox. Sign up today.