The commission, over a series of 12 public meetings for the next two months, will be examining the experiences of the public and staff in the health service.
The inquiry, thought to be the first of its kind, was announced following a major incident at the Royal Victoria Hospital.
Over 100 patients faced long waits to receive treatment while staff described the scene as like a war zone.
On Thursday, the commission officially begun the process with its first public meeting.
However, DUP Health Minister Edwin Poots questioned the need for the inquiry.
He told UTV: "I don't welcome the inquiry, sometimes you can have too many inquiries going on at one time. Nonetheless, I will co-operate with it."
Following January's major incident at the Royal the Regulation and Quality Improvement Authority (RQIA) and the former chief medical officer for England are conducting their own investigations of emergency health care provision across Northern Ireland.
Edwin Poots added: "The RQAI is an independent body carrying out the same work and Sir Liam Donaldson is a true expert in the subject. So I am sure we will get to the bottom of the issue."
Paul Hunt, a former United Nations investigator with a speciality in health who is part of the commission's inquiry, said the process would add to the other probes.
With human rights being so closely aligned to the work of health care professionals, it is only right we look at this from a human rights perspective.
Paul Hunt, former United Nations Special Rapporteur
He said: "The inquiry and the eventual report will do something different. It will take a human rights-based approach to the issue.
"We will be looking at good quality treatment and the right to dignity and respect.
"Most important is that this process is participatory and will allow health staff and the public to tell us their views."
He added: "The issues have been troubling and this process will, we hope, contribute to positive changes and will make specific recommendations which will contribute to making things better.
"Its findings will be of interest at an international level, particularly to those in the UN who monitor these things and it will be of interest I am sure."
Les Allamby, head of the commission, added: "Over 700,000 people attend accident and emergency services every year in Northern Ireland.
"We expect to hear from people who have had positive experiences as well as those who have not. The aim of this inquiry is to have an improved emergency healthcare system in Northern Ireland, one that maintains human rights best practice."
The Commission will publish its final report and recommendations to the Northern Ireland Executive in April 2015.
This inquiry is about hearing from the people who use and work in our emergency care system. We want to identify what works, so it can be repeated, and what does not, so it can be improved.
Les Allamby, chief commissioner NIHRC
Deirdre Dougal suffers from a range of serious illnesses including diabetes, a thyroid problem and heart disease.
She made submissions to the commission's first public hearing on Thursday.
The wife of the late journalist Jim Dougal, was faced with a 17 hour wait when she visited the Royal Victoria Hospital's emergency department in February.
She argues the health department should not get more cash until it can promise improvement in service.
"When I was in hospital my children were told I was criticall ill, but no one told me anything," she told UTV.
"I never saw a doctor and had no idea what was wrong or what was happening.
"I had drips in my feet so could not even move about the ward, I was stuck in the trolley."
She added: "I want to see something come from all these reviews.
"Every profession is facing cutbacks and people have to work within their means.
"But the hospitals just seem to do what they like, they don't appear to be accountable to anyone.
"I would want to see what changes they are going to make before they get any more cash. I want to know I won't have a 17 hour wait again."
In a statement, the Belfast Health Trust said: "We are sorry Mrs Dougal had a poor experience.
"We know we have challenges in delivering emergency department services and we are on a major journey of improvement.
"We are determined to ensure a better emergency department experience for all our patients and their families."