Indonesian's government has been urged to ensure that state security forces who attack journalists in regions like Papua are held to account.
The call from the NGO Human Rights Watch comes as Indonesia prepares to host a series of events for World Press Freedom Day on Wednesday.
It points to new research data from Indonesia's Alliance for Independent Journalists showing an increase in assaults on journalists in the past two years in Indonesia.
At least a dozen cases in this time refer to journalists being attacked, intimidated or detained in Papua region, otherwise known as West Papua
The Alliance says foreign journalists and local fixers are liable to be arrested and prosecuted if they try to document the Indonesian military's abuses there.
However, since the election of President Joko Widodo in 2014, Indonesia's government has been making steps towards opening up Papua region to foreign journalists.
After Mr Widodo "lifted" the effective ban on foreign journalists visiting Papua, several foreign journalists went to Papua in 2015, including two from RNZ International.
But, numerous restrictions remain on foreign media access to Papua.
The international media watchdog, Reporters Without Borders, this month called on Mr Widodo to keep his promise to allow foreign journalists to operate in Papua without obstruction or surveillance.
The organisation said Jakarta's repeated refusals to issue press visas and the growing number of journalists on its blacklist, showed it fell far short of qualifying as a country that supports freedom of expression and media freedom.
But as Jakarta hosts World Press Freedom Day on Wednesday, abuses against local journalists remain the most pressing media issue in Papua.
Numerous journalists working with the independent Papua-based newspaper Tabloid Jubi have been subject to threats and attacks by security forces in recent years.
Indonesian law also requires journalists who are targets of physical assault to report such incidents to the National Police Profession and Security Division if the perpetrator is a police officer, or to the Military Police if the perpetrator is a soldier.
However, the government human rights commission, Komnas-HAM, has found that police investigations of incidents of violence against journalists often stall "because of technicalities or as a result of social or political pressure."
After interviewing numerous journalists and human rights advocates across Indonesia, Human Rights Watch said they described "an atmosphere of fear and self-censorship in many newsrooms".
It said this was "due to abuses and threats by security forces and local authorities that go unpunished and that, most of the time, are not even rigorously investigated".
According to the NGO, Jakarta must show it is serious about press freedom by ensuring accountability for these abuses.
This echoed a call by Irina Bokova, the director general of the United Nations Educational, Scientific, and Cultural Organization, which chose Jakarta as global host for its annual World Press Freedom Day commemoration.
She said Jakarta should use the occasion to publicly address the increase in assaults on journalists and urge President Widodo to take more decisive action in response.
Meanwhile, difficulties around press freedom in West Papua are the subject of a discussion event in Jakarta tomorrow, ahead of World Press Freedom Day.
This event will feature discourse by Tabloid Jubi's founder, Victor Mambor, the head of Indonesia Amnesty International, Usman Hamid, and David Robie, lecturer at Auckland University of Technology and founder of Pacific Media Watch.