The application, filed on behalf of Kurdish refugee Behrouz Boochani, had sought to ease a standoff at the Manus Island immigration detention center which started last Tuesday, when the center was formally closed.
Food, water and power was cut to the site, and the refugees, who fear they'll be attacked by locals if they leave, have been surviving off water dug from their own well.
"Depriving refugees from having access to basic and vital things is completely against humanity," Boochani told CNN by text after the ruling.
"This order shows how we are forgotten people and there is no justice for us," said Boochani, who was sent to the Australian-run immigration processing center in 2013 after fleeing persecution in Iran.
While the Chief Justice found Boochani's human rights may have been breached, he indicated that new facilities being provided for the refugees would remedy the situation, Barrister Greg Barns told CNN after the ruling.
The refugees, however, say their issue is not with the new facilities, but the security surrounding them. Unlike the existing facility, which is located on a secured site far from residential areas, the new facilities are located in the town of Lorengau.
The refugees fear being attacked by angry locals who don't want them living in their town. In the past, they've been slashed with machetes and robbed of their mobile phones, according to the men and recent Human Rights Watch report.
Lawyers will be visiting the new sites to see if they're suitable and, if not, will challenge the ruling, Barns said.
Protests during Melbourne Cup
Prior to the ruling, refugee advocates staged multiple protests across Melbourne to attract the attention of Australians celebrating the annual Melbourne Cup horse race.
The annual sporting event is a major occasion across Australia, referred to as "the race that stops a nation,"
and attracts tens of thousands of attendees as well as millions more watching on television and online.
Two women climbed to the top of a crane within sight of Flemington racecourse, where the race is held, and unfurled a banner reading "SOS -- Evacuate Manus Now."
Meanwhile protestors parked a car across the train tracks carrying racegoers towards Flemington, covered in writing which read "Evacuate Manus."
Video posted by CNN-affiliate Seven News showed the activists at the train track being arrested by police, while photos on social media showed officers climbing the crane to arrest the other protestors.
Victoria Police posted on their social media a notice saying they had increased patrols at the racecourse in response to the ongoing protests across the area.
No resolution in sight
For months, the refugees and asylum seekers -- all men -- have been warned to leave the center ahead of the October 31 closure and move to the three new centers.
Rights advocates reacted with outrage to the ruling, which they said was exacerbating a humanitarian crisis.
"The decision of the PNG Supreme Court decision does not alter the inhumanity of the siege on Manus Island, nor alter the role of the Australian government," said Ian Rintoul, spokesperson for the Refugee Action Coalition.
"It does not alter the fact that Manus is unsafe, and settlement in PNG is impossible. The onus is still on the government to provide the safety and security that the refugees and asylum seekers need."
Elaine Pearson from Human Rights Watch said the men need urgent food, water and medical care, and that it was Australia's responsibility to bring them to safety.
"(Australian) Prime Minister Turnbull can't turn a blind eye to the well-founded safety concerns these men have. Moving hundreds of men to a town where refugees have been beaten, stabbed and robbed is incredibly irresponsible," she said.
PNG police have been preventing anyone from approaching the center with food supplies, under the orders of the Commanding Officer of the Lombrum Naval Base.
"Police and Military Police are enforcing the Commanding Officer Directives to deal with unnecessary people coming into the base to feed the refugees at the center," Chief Superintendent Dominic D. Kakas said in a statement Monday.
The Australian government has said the men had been clearly warned for months that food and other necessities would be cut off after October 31, and that they should move to alternative accommodation.
The center closed after a PNG court ruling last April that the mens' detention breached their right to liberty.