A respected Mexican newspaper has asked drug cartels for guidance on how not to offend them following a photographer's murder, deepening alarm that drug-related violence has stifled media freedom.

El Diario de Juárez, the leading daily in the border city of Ciudad Juarez, published a front-page editorial yesterday titled "What do you want from us?" – addressed to the narco-traffickers.

Calling them "señores", the paper asked what news it should and should not publish following last week's shooting of a photographer, the paper's second murdered journalist in two years.

"We want you to know that we are communicators, not mindreaders. We do not want more deaths. It is impossible to carry out our role in these conditions. Tell us therefore what is expected of us."

In a blunt admission of Juárez's lawlessness, it said: "You are, at present, the de facto authorities in this city because the legally mandated authorities have not been able to do anything to keep our colleagues from continuing to fall, although we have repeatedly demanded they do so." Even in war, there are rules to protect media workers, it added. "Therefore explain to us what is wanted of us in order to stop paying the price with the lives of our colleagues."

The paper, which until now has chronicled the US border mayhem in detail despite fear and intimidation clamming up other media organisations, was shocked by the 16 September gunning down of Luis Carlos Santiago, 21, a photographer, and the wounding of an intern, as they left the office for lunch.

El Diario had not decided to censor reporting, for now it merely wanted to know what cartels considered out of bounds, Rocio Gallegos, a news editor, told the Guardian. "We want to know what their view is and that will inform our decision-making." The editorial was aimed as much at the government as drug lords, she said. "We are alone here. There is no state of law." Neither officials nor narco-traffickers had yet responded, said Gallegos. "We have no idea if we are going to get any answer."

El Diario is still awaiting a conclusion to a high-profile police investigation into the 2008 murder of a crime reporter, Armando Rodríguez, who was shot in his car outside his home. Of an estimated 6,400 murders in Juárez in the past two years only a handful have been solved.

Impunity was underlined by the release last Saturday of four men – who were recently paraded before the media and accused of 55 murders – for want of evidence. Despite a relatively small population of 1.3 million, the city, a smuggling point which borders El Paso, accounts for a large chunk of the 28,000 killed in Mexico since President Felipe Calderón declared war on the drug cartels in 2006.

Around 30 media workers have disappeared or been killed, some of them tortured and mutilated, making Mexico one of the world's most dangerous places for reporters.

"The widespread and unpunished attacks are destroying citizens' constitutionally and internationally protected right to free expression," the Committee to Protect Journalists, a US-based advocacy group, said in a recent report.

Many print and broadcast outlets have restricted coverage of drug violence to brief accounts that avoid identifying organisations and individuals. In some cities, notably Reynosa, shoot-outs in broad daylight go completely unreported.

El Diario, which has just one armed guard in its lobby, continued reporting Juárez's troubles, a conflict pitting the Sinaloa cartel against a homegrown group, as well as overlapping battles involving hundreds of criminal gangs and rogue police officers and soldiers. In the absence of detailed official statistics, the newspaper's "board of death" – a tally updated daily with a blue marker – is one of the few ways to track the bodycount.

Since Carlos Santiago's murder, the board has noted dozens more deaths, including a massacre in a city centre bar and the beating and hacking-up of a 52-year-old woman and her 14-year-old son in Juárez valley.