It is considered one of the world’s most beautiful islands, a still-not-totally-discovered destination where tourists can frolic on white sands by day and sip cocktails by night in seafront villas. There are clubs playing house music, jetskis glistening in the afternoon sun, and yachts moored in the distance. It inspires the most cliched of descriptions – “paradise on Earth”, “the world’s best island“ – yet for the Atis, who claim to be the original inhabitants of Boracay in the Philippines, life is a daily struggle.

From a squashed compound of dusty vegetable plots and thatched huts separated from the main road by a flimsy bamboo fence, this indigenous tribe of 200 families is fighting for its right to live and work on the island. Largely uneducated and desperately poor, the Atis say they have been pushed off the land they have lived on for centuries by the hundreds of hotel chains, bars and businesses cashing in on Boracay’s multimillion-dollar opportunities.

Now they also fear for their lives. In February, the Atis’ youth leader and spokesman, Dexter Condez, 26, was shot with a submachine gun while returning home with two others from a meeting about land. The assailant ran off into the dark night. Witnesses identified the gunman as Daniel Celestino, 27, a security guard at the Crown Regency resort. Celestino has been charged with murder, but both he and the resort owner deny any involvement.

“We never believed it would come to this,” said the Ati chieftain, Delsa Justo, 54, a gaunt woman with a serious gaze and pink comb sticking out of her curly hair. “Only one thing is for sure: this is about the land.”

After years of being evicted from one end of the island to the other, in 2011 the tribe won a government-issued certificate of ancestral land title on a 2.1-hectare seafront site – prime real estate potentially worth up to £800 per sq metre. But three other claimants, among them property developers, hotel owners and investors, contested the decision, saying they owned partial, or full, rights to the site. One claimant – J King and Sons, which operates three hotels in Boracay, including the Crown Regency resort – already had big plans for the land granted to the Atis: 50 villas with a yacht club, and exclusive snorkelling and diving access.

Not long after the tribe moved on to its newly won ancestral land, armed security guards from the Crown Regency came to tear down a fence the Atis had built there, claiming the land belonged to the hotel instead.

Then Condez was gunned down and Celestino was charged with his murder.

But under Filipino law, suspects have to be arrested within two days of their alleged crime in order to be searched. As it took officers a few days to find Celestino, he has still not been subjected to tests, nor has his property been searched, and little evidence has been collected to support the case. For days leading up to his murder charge, he was still working at a “jungle bar” abutting the Atis’ plot. “He was just sitting there, looking at us,” one Ati told the Guardian.

Celestino could not be reached for comment. But in a 20-page counter-affidavit sent to the Guardian by his lawyer, Celestino claimed he was working the night of Condez’s death and called the charges against him “absolutely false, malicious and unfounded” and “unworthy even … of a telenovela or work of fiction”. He also suggested that he, and the witnesses, subject themselves to a polygraph test “in the interest of truth”. Celestino’s lawyer, Augusto Macam – who also represents the Crown Regency in its dispute with the Atis – stressed that “my client [is] totally different from the description given by the alleged witness to the fatal shooting of Dexter Condez”.

Richard King, chief executive of the Crown Regency hotel chain, said the resort had to defend its boundaries from the Atis, who “squat over”, but denied any involvement in Condez’s death.

“If you were on our side, would you be happy if someone just fenced on your property, encroached on your property?” he asked. “The media is all portraying us to be the bad guys … but it seems the police were pressured by the media. But our guard is innocent. He’s not lying. He’s not afraid.”

Still mourning the loss of their spokesman, the Atis have continued to fight for both land and justice. “He [Dexter] was killed because he was very brave – brave enough to face the people who were harassing us,” said Condez’s aunt, Evelyn Supetran, 38. “Now we must face them.”

A well-known figure in Boracay, Condez represented the Atis at indigenous peoples’ conventions, acted as the voice of the community on the island and promoted self-empowerment. By encouraging Ati teens to continue their studies, find jobs and participate in a monthly cultural evening during which the elders would share their oral histories, Condez hoped to fight the stigma that had plagued the Atis for decades – that they were dirty, dumb and worthy of being disregarded.

“They have experienced discrimination all around the island,” said Chaya Go of the Assisi Development Foundation, a Filipino organisation helping to strengthen the Atis’ community. “They are called ‘eyesores’ because apparently they’re not ‘nice to look at’. Whenever their kids would swim along the shore, if there was a nice restaurant or hotel established there, they would shoo them away.”

Property is a booming business in Boracay, whose £350m tourism industry has soared from a handful of visitors in the 1970s to 1.2 million today – and politics and land are often intertwined. The current mayor, John Yap, and some of his predecessors are said to own some of the island’s top multimillion-dollar resorts, most of which hire private security guards to police their property boundaries. Only a third of properties on Boracay island currently hold land deeds – the rest are the subject of tax declarations – and shootouts between security forces are so common that property disputes now take up the majority of police officers’ time, said senior inspector Joeffer Cabural.

“This is the problem with security guards: they are taking risks and losing their lives because of someone else’s war,” he said at Boracay’s seaside police station. “The persons [actually] involved are huge businessmen who have a network [all the way up] to national government.”

Cabural, who is in charge of the investigation into Condez’s death, said police were working with the national bureau of investigation to find a second assailant involved in the murder. The justice ministry has called for the case to be fast-tracked in Manila’s famously slow courts, although little headway seems to have been made.

A regional court recently banned the construction of permanent housing on the Atis’ site after one of the claimants filed a cease-and-desist order.

“Why does the court keep ruling in favour of the claimants? They don’t have rights to the land – it belongs to the Atis,” sighed Sister Herminia Sutarez, a nun who has worked with the Atis for the past five years. “Now it will take years, we don’t know how many years, until it is settled.”

Although local papers often run editorials complaining of Boracay’s existing overdevelopment, some property developers have lofty goals for the island – from water parks to luxury villas – and the Crown Regency aims to be at the forefront of that expansion.

“We will change the way Boracay is enjoyed,” King announced in January. “We will continue to build great amenities so that, in the following years, it is not only Boracay [that] will be recognised but the whole Philippines as well, because of Crown Regency.”

For the Atis such as Justo – who remember an island where the beaches “had no hotels or buildings, we could bathe nude in the sea, and we would hunt wild boar, monkeys, turtles and lizards” – further development will come at a cost. Most families already live below the national poverty line and only a fraction have jobs – mostly in manual labour, building tourist resorts. Squashed on to a small plot in Manoc-Manoc, their land concession feels like more of a prison than an opportunity. Few visitors enter, and few inhabitants go out – in fear, perhaps, that if they do, claimants may steal their land away. Many of the men drink, and part of the reason that a 24-hour police outpost is located just across the street from their community, according to Cabural, is to prevent domestic violence.

But a noticeable change has taken root in their community, activists say, as their fear has been replaced with defiance. “After Dexter was killed we were threatened,” said Justo. “We thought if we walked along the beach we’d be targeted. But now we feel like we gain strength from one another. Now we stand up.”