The Papua Justice and Human Integrity Foundation has reported multiple Indonesian military sweeps responsible for acts ranging from physical assaults to other forms of intimidation and interrogations in one of the troubled regencies in the Papua Highland province.

A monitoring report has highlighted a troubling two-day period, which was based on accounts from witnesses and residents.

The allegations surround the military's search for a West Papuan independence fighter.

It is alleged Indonesian military personnel seized personal belongings from residents during operations across four districts of Tolikara regency.

Soldiers entered the Gundagi District in the early hours of the morning last month, firstly breaking into a man's home, who is blind with a long-term physical disability affecting both legs.

The man, who was lying in bed, heard the soldiers and raised both hands surrendering after several doors were allegedly broken down.

Several items were taken from the house that included company documents belonging to the man's brother.

They questioned the unnamed man about the whereabouts of Botak Wanimbo, a publicly known figure associated with the territory's armed pro-independence movement.

One soldier allegedly struck the man four times on the forehead with a large screwdriver, while another soldier reportedly hit him three times on the back with a fan belt.

The soldiers allegedly left with air rifles belonging to other Gundagi community members in addition to the man's own identity card, mobile phone and bank passbook.

According to the report, several other people were inside the house, including the blind man's father, an elderly Christian minister, two women with their four children.

Three soldiers allegedly pointed firearms at the man's father, demanding information about Mr Wanimbo.

The report said one of the men was ordered to place his hands on the floor as a soldier attempted to stab him with a knife.

That man, who pulled his hands away, was then taken outside with his eyes covered by a cloth, as soldiers allegedly took turns harassing and intimidating during questioning about Mr Wanimbo.

The report alleged the incidents formed part of a wider series of searches and interrogations in the area.

Soldiers allegedly visited homes the next night in Kembu District, ordering 20 residents to come outside.

They also were reportedly questioned about Mr Wanimbo, including while detaining a pastor.

The wife of the pastor was preparing food when three soldiers entered their home and asked about her husband.

He returned from praying only to be asked about Mr Wanimbo.

The Papua Justice and Human Integrity Foundation has called for an independent investigation.