He shakes as he speaks and at moments his eyes fill. "It's certain that the people who killed my colleague were criminals," he says. "The killing had the modus operandi of organised crime. But who sent them and why? That's the question, that's the smokescreen."

This is a colleague of Víctor Manuel Báez Chino, whose mutilated body was found in June in the main square of Xalapa, capital of the Mexican coastal state of Veracruz. Báez was the state's crime editor for an online edition of the national newspaper Milenio and editor of the Police Report website (currently down) which covered crime.

In August, state prosecutors declared the case closed. Witnesses, they said, had identified the bodies of two men killed in a shootout as the same people who had kidnapped the reporter. Báez's circles were "entirely unconvinced", says his colleague.

Báez is one of 56 journalists killed during Mexico's drug war since 2006 (a figure calculated by the New York-based Committee to Protect Journalists). The war reached a climax last week with the killing by Mexican marines of the leader of the wildest – albeit not the biggest – narco cartel: the paramilitary Zetas, which counts Veracruz, with its strategically crucial gulf port, among its strongholds.

After a spate of further killings this year, Veracruz became the focus for this war against the press: six reporters were killed in Mexico within a month leading to mid-May, three of them in Veracruz.

This is no sideshow in a wider war involving the drugs cartels, argues the committee's representative in Mexico, Mike O'Connor. He insists that "the silencing of the press and killing of journalists is integral to the reality, the big story, of what is happening here: that the cartels are taking territory".

Furthermore, he says: "The inability of the government to really solve hardly any of the crimes against journalists during the four years I've been here is a metaphor for its inability to solve crimes against common citizens. They simply cannot do it. And you wonder: if they can't solve these crimes, why not? Is it because they don't want to?"

Of course, the threats and killings proliferate beyond Veracruz, across Mexico. In the border town of Nuevo Laredo, Ramón Cantú, publisher of the local El Mañana, said, after his paper's offices were attacked by the Zetas: "We are censoring the paper because we have to get our children to school." In Ciudad Juárez, my friend Sandra Rodríguez is among the reporters who work on bravely, despite the killing of two colleagues, "because we have to carry on with this task, to expose what is going on".

Among those brutally killed in Veracruz was Yolanda Ordaz de la Cruz, whose decapitated, tortured body was found in July last year, dumped near the offices of her newspaper, Imagen, two days after she was seized by armed men as she left home.

State prosecutor Reynaldo Escobar Pérez insisted the killing was not linked to her work and state governor Javier Duarte de Ochea said authorities were pursuing "multiple lines of investigation". Another was Miguel Angel López Velasco, columnist for the daily Notiver, who was killed along with his wife and son the previous month.

Apart from the barbarism of his killing, Víctor Báez's death bore another hallmark of a narco execution: a note pinned to his torso, this one reading: "Here's what happens to traitors and people who act clever. Sincerely, the Zetas." But Báez's colleague says that he learned from the marines "that the note was not there when the body was discovered by a neighbour who found Víctor's door open – it was put there later… by someone, for some reason". All of which compounds the strangeness of Báez's death, the explanation for which anguishes his colleague, as we sit in a cafe, shielded by the sound of the grinding of fresh coffee grown in the hills beyond the city.

"He had no connection to the cartels. Víctor knew how to stay independent. I was one of the last people to see him – he seemed tranquil, he had nothing to do with the government or the narcos." But Báez did know some background to the most infamous murder of a reporter in Veracruz: that on 28 April this year of Regina Martínez, a friend of his.

Martínez was Veracruz state correspondent for Proceso magazine, by repute one of Mexico's most prestigious. She was found dead in her lavatory, beaten and strangled to death.

"Others have died in worse ways than Regina," said a friend and one-time source of Martínez in Xalapa last week. "In some ways, I'm amazed she wasn't killed before. She was working for some time on dirty police" – and her voice trails off. "Regina was a good friend of mine and one of the few who dared to write about what is happening here."

There has been public outrage in Veracruz over Martínez's murder, as there has been across Mexico at the others. Martínez's killing provoked street demonstrations demanding that the perpetrators and those who gave them orders be brought to justice. On Saturday in Xalapa, an assembly was hosted by a new student movement in Mexico, I Am 132, with local reporters, to discuss common cause and strategies for mutual protection.

I Am 132 is so called after 131 students appeared on YouTube to give their names and ID numbers and deny allegations that they had been paid to disrupt a meeting addressed by the incoming Mexican president, Enrique Peña Nieto. The skirmish had been over development of land for an airport, but the movement expanded into narco war, free speech and assaults on the press.

"At first, we thought the reporters were part of the problem," says the movement's humblingly brave young spokesman in Veracruz. "Then we saw the big picture, and how it must be for them, and the idea this weekend is for an assembly that can work towards a safety network of some kind."

Into all this, last week, the Mexican branch of the Hay-on-Wye literary festival arrived – Hay Xalapa – guest of the state government. Hay had been criticised from some quarters for accepting the hospitality, but rode it to stage an event of intellectual effervescence and allow the opening of an international window to Xalapa's journalists. Representatives of the freedom of expression group PEN arrived to make preparations for a campaign over the murder of reporters in Mexico, to be launched on the next Day of the Dead, on 2 November.

The president of PEN America, Peter Godwin, found himself present at an unexpected photo opportunity between state governor Duarte and Nigerian poet and playwright Wole Soyinka. Godwin petitioned the governor "to express", he said afterwards, "PEN's grave concerns about the killings of journalists in Veracruz in particular and the climate of impunity in Mexico generally. I concluded my questioning of the governor by saying that I hoped that there would be no more journalists killed in Veracruz province between this Hay and the next."

(To complete the surreality of the occasion, Proceso magazine posted on its website a detailed account of a supposed meeting in the Crowne Plaza hotel in Xalapa, at which Duarte supposedly "exploded" with recrimination at Godwin, esteemed American writer John Lee Anderson and me for speaking badly of Veracruz. The story was a fabrication – denied by the governor's office and all three of us. )

It happens that the Committee to Protect Journalists is represented in Mexico by one of America's most experienced and renowned reporters. Mike O'Connor is a veteran of the "dirty wars" in Central America during the 1980s for CBS television and of other conflicts thereafter for the New York Times. For nearly four years now, he has documented and investigated the intimidation and murder of Mexican reporters and toured the country consulting those under threat. He is uniquely qualified to explain how the war against the press speaks to Mexico's carnage.

"The government and authorities are ceding territory to the cartels and, for the cartels to take territory, three things have to happen," says O'Connor. "One is to control the institutions with guns – basically, the police. The second is to control political power. And, for the first two to be effective, you have to control the press.

"Every journalist I've spoken to says that the corruption of forces is such that the cartels control the politicians. That does not say that the cartels get money from this – there are rewards for the politicians and there's a very strong disincentive not to co-operate. I'm not quite sure what the word is to describe the relationship, but ultimately the capo is in charge."

However: "When I… say to a roomful of journalists, 'Ask the question, Quien manda aquí? (Who's in charge?'), they take a virtual step backwards, wide-eyed. That's the question you ask yourself at night when you're drunk and your wife is asleep and you hope no one hears you."

O'Connor argues: "You can't have a democracy without an informed public… Mexico has all the structures of a democracy, but it does not have an informed public. It has a public which knows the starting lineup of the Green Bay Packers, but doesn't know who runs the city or the state they live in. It does not know who is in charge. People know it's corrupt, but they don't know what's going on, because the reporters cannot ask: 'Who's in charge?' You cannot find in your newspaper, in most parts of the country, information about the big story – and the big story is that organised crime has taken over, or is working very successfully at taking over, your city, town or village.

"And if you report that, you get killed. Mostly, you don't think about reporting that."

O'Connor summarises government officials as insisting that all Mexican journalists are corrupt and the victims are working for the cartels – "as if they could possibly know". Working on the ground, he says: "Look, I don't have the FBI crime lab behind me – I do the investigations I can within the environment I have. And I know that at some times and in some places, a reporter might get approached by someone with a pistol, and told to write this but not that, and there may be some money in it. And if you don't, we know where you and your family live.

"Is that working for the cartel? Federal officials use that context to make out that the dead are working for the cartels. I know reporters who get asked by the police chief, 'Why are you so curious?' That's a threat."

However, he says, "the people I know in Xalapa say that Regina Martínez was looking into the political and economic elite. That is what she wrote about". Then O'Connor qualifies the judgment, only slightly, with a favourite dictum of his, that "Mexico is a country where you do not need facts to arrive at a conclusion. People will hold on to a belief without being able to give it a factual basis. But that does not mean it is not true."

The atrocious news arrived just as the Hay festival left Xalapa: that while it was in town, another reporter from a journalistic family, and his daughter, had been killed – both decapitated. Roberto Rizzo Murrieta who worked for the Mundo de Córdoba paper, was murdered at home with his child, María Antonia. The state prosecutor said again that "multiple lines of investigation" had been opened and a domestic employee was under suspicion.