Marni Cordell – At least one person was killed and others injured when Indonesian police opened fire and beat activists during a demonstration in the West Papuan capital of Jayapura last week, according to a witness.

The witness, who asked not to be named, said police fired live bullets into a crowd of about 800 demonstrators and also beat people with their firearms at a political rally last Tuesday.

The body of West Papuan man Matias Tengket was later found in a nearby lake, the witness said. "Tengket's body was thrown into Sentani Lake after being killed [by police]."

An eyewitness to the murder told independent West Papuan news outlet, Jubi, that Tengket was chased down and beaten to death by a group of people driving a black Avanza car. They then dumped his body in the lake.

But the head of Jayapura police, Alfred Papare, said Tengket's body was later examined at a police hospital and found to show no signs of mistreatment.

When asked if police shot Tengket, Papare replied, "[The deceased] didn't have any injuries whatsoever. There was no maltreatment of him let alone him having been shot. The finding of that body has no connection with the ... demonstration".

The witness said the confrontation occurred when police took a vehicle that was being used to carry a sound system and ordered the crowd of demonstrators to stop marching and enter a nearby building. When they refused, "hundreds of police blocked the crowd moving down the road", the witness said. Police then started shooting into the crowd.

"We thought it was tear gas they were shooting, aiming towards us. We became frightened and the crowd including myself fled. But then we realised it wasn't tear gas they were shooting at us but rather they were firing bullets from weapons."

The police chased the fleeing demonstrators and "there were many that were injured," the witness said.

He told Guardian Australia he escaped injury by hiding in the house of a family until the police had dispersed, and said police had given public orders for people not to hide the demonstrators, many of whom are now in hiding in fear for their lives.

Parpare denied the use of live fire at the demonstration and said "the demonstrators didn't have a permit, so they had to be dispersed". "In any demonstration whatsoever the police never fire weapons. The only firing by police was of tear gas," he said.

The rally was organised by the West Papua National Committee (KNPB), an organisation that campaigns for a referendum on West Papuan independence.

In a statement released last week, the KNPB's general chairman, Victor Yeimo, said other activists involved in the action were still missing, presumed dead.

"[We are] looking for four other KNPB members that are missing: their whereabouts are unknown. We strongly suspect that the police shot them and disposed of their bodies."

On Thursday, Amnesty International released a statement calling for an investigation into reports that 28 political activists who were arrested at the rally had injuries consistent with being beaten in custody: "According to a human rights lawyer who saw them in detention at the Jayapura City police station, there were indications that they had been beaten after they were arrested."

"The authorities must ensure a prompt, thorough, and effective investigation into the allegations of ill-treatment by the police and ensure that those suspected of involvement, including persons with command responsibility, are prosecuted in proceedings which meet international standards of fairness," the statement said.