In a strongly-worded statement issued on Monday, Filippo Grandi said UNHCR had agreed to help with the relocation of refugees on Manus Island and Nauru to the United States last November when the deal was struck, AAP reported.
But that was based on the "clear understanding" that vulnerable refugees with close family ties in Australia would ultimately be allowed to settle there.
"UNHCR has recently been informed by Australia that it refuses to accept even these refugees," the UN's high commissioner for refugees said.
That meant some with serious medical conditions or who have experienced trauma including sexual violence can't get support from family in Australia.
"To avoid prolonging their ordeal, UNHCR has no other choice but to endorse the relocation of all refugees on Papua New Guinea and Nauru to the United States, even those with close family members in Australia."
The agency claims the understanding was reached over a number of months in a series of meetings and correspondence involving government officials.
But it's unclear who exactly gave the undertaking.
UNHCR's assistant high commissioner for protection Volker Turk said Immigration Minister Peter Dutton and his department had agreed to allow compelling cases to be presented for consideration.
"It is on the basis of that understanding that we made these cases to the Australian government in the hope that, as is normally the case in such instances, those with close family links would be able to settle in Australia," he told ABC's 7.30 program.
He said only 36 people so far have been identified as having close family links to Australia.
The claim stands in stark contrast to the message the Turnbull government has been peddling publicly.
Dutton's office, in dismissing the accusation, reiterated that those transferred to offshore processing centers will never settle in Australia.
"The position of the coalition government has been clear and consistent," a spokeswoman said.
On Sunday, Dutton said there was no contingency under which the government would change its mind.
"No, and people will not be coming to Australia," he told Sky News.
Grandi said there was no doubt vulnerable people - already subject to four years of "punishing conditions" - should be reunited with their families in Australia, labelling it the humane and reasonable thing to do.
"The Australian government's decision to deny them this possibility is contrary to the fundamental principles of family unity and refugee protection, and to common decency," he said.
He urged Australia to bring an immediate end to the harmful practice of offshore processing, claiming it has caused extensive and avoidable suffering.
His sentiments have been echoed by Amnesty International, Human Rights Watch, the Human Rights Law Centre, Refugee Council of Australia and the Asylum Seeker Resource Centre, who have all called on the Turnbull government to reunite those families who have been split up.
"That the UNHCR chief issued such a stinging rebuke of Australia's policies speaks volumes - the UN is sick and tired of Australia shirking its responsibilities under international law," Human Rights Watch's Australia director Elaine Pearson said in a statement.