Pillay issued a sharply-worded statement a day after Iraq put 21 men to death for terrorist offences, bringing to 50 the number of executions Baghdad has carried out so far this year, despite widespread calls for a moratorium.
"Executing people in batches like this is obscene. It is like processing animals in a slaughterhouse," said Pillay, pointing to reports that a further 150 people could be executed in coming days.
"The criminal justice system in Iraq is still not functioning adequately, with numerous convictions based on confessions obtained under torture and ill-treatment, a weak judiciary and trial proceedings that fall short of international standards," she said.
"The application of the death penalty in these circumstances is unconscionable, as any miscarriage of justice as a result of capital punishment cannot be undone," she added.
A total of 1,400 people are believed to be currently on death row in Iraq, and 129 people were executed in 2012 alone, Pillay's office said.
Her spokesman Rupert Colville said it was not clear why the number of executions in Iraq was spiking.
"There were years where there were hardly any or no executions, three or four years ago," Colville told reporters.
"Obviously, Iraq is suffering still from many acts of terrorism, many bombs, atrocities continue to take place there, but that doesn't warrant executions on this kind of scale, or executions at all, necessarily," he said.
"It's extremely deplorable, and depressing, that this kind of conveyer belt of executions continues," he added.
Iraq says that it only executes individuals convicted under its 2005 anti-terrorism law who have committed terrorist acts or other serious crimes against civilians.
Pillay said the law was too broad in scope.
"I am the first to argue there must never be impunity for serious crimes. But at least if someone is jailed for life, and it is subsequently discovered there was a miscarriage of justice, he or she can be released and compensated," she added.