He said any plans for the future of residential care homes must have a "clear pace of change" and that any threat of closures over the next six months is gone.
Minister Poots was updating the assembly on plans for caring for older people following an emergency meeting on Friday.
It was called following public outcry over some Health and Social Care Trusts' plans to close all of their residential care homes.
"I do not want to see any older person distressed about the future," Mr Poots told the assembly.
"But I know that several older people have been upset by the proposed changes and I want to apologise to them for any unintentional stress that may have been generated by these consultation proposals."
The minister told MLAs that there "never was any question of making anyone homeless or of enforcing change in any draconian way".
No-one can disagree with the policy that home is the hub of care. But how we achieve this, needs to be carefully planned and communicated, and those older people currently residing in statutory residential homes must be listened to, and treated with sensitivity and dignity.
Health Minister Edwin Poots
The minister's apology came as those opposed to the closures were still out in force.
A protest took place outside Rectory Fields Care Home in Londonderry, one of four earmarked for closure in the Western Trust area.
Those campaigning fear the minister's intervention is merely a stay of execution.
Mr Poots continued: "It was very unfortunate that the clear positive intentions of the policy became lost in the distressing sequence of stories over the last two weeks and it is now essential that we put public assurance and confidence at the top of the agenda.
"But I would also hope that some of the positive changes that Trusts were proposing can proceed. Their intention and mine is to improve services and move away from a model of care that is no longer the best available and which involves many people living in homes that do not meet the standard expected."
The minister said he was fully in support of Transforming Your Care, in its aims to promote independence, social inclusion, re-ablement, and support in the community for as long as is possible.
"The process of engaging with older people, their families and the public has got to change and the pace of change needs to be planned in a coordinated way across all of the Trusts. That was not clear, therefore on Friday 3 May, I called a halt to individual trusts consulting on proposed closures within the area," Mr Poots said.
"We will now make a fresh start. I've asked the HSE board to lead on a new process for consulting and implementing change. I expect the HSE board to work closely with trusts to coordinate a regional approach on residential care homes with trusts having more time to engage with individuals, families, communities and staff."
We accept that there are areas of our Health and Social Care Systems that need reformed but we are also mindful at the shift from patient-centred care to profit driven care.
Conall McDevitt, SDLP MLA
Mr Poots said he wanted assurances from the Board that best practice will be followed in the future development of proposals.
He added that any changes were likely to be carried out over a much longer period of time and that the 330 people directly affected by any potential changes should have their say on the process.
Reacting, Sinn Féin West Belfast MLA Sue Ramsey said the Health Minister must ensure that the needs and well-being of those affected are paramount prior to any further implementation of Transforming Your Care.
The Chair of the Assembly's Heath Committee said: "The fear and distress caused by the care homes fiasco must not be repeated and the minister must ensure such a mess does not happen again and that any confusion between his department and the Health Trusts are, unlike this time, cleared up immediately.
"Transforming Your Care is being introduced to make our health system better and bringing that care into the community. The mess surrounding the care homes announcements plainly shows that the minister has taken his eye off the ball and that is unacceptable."
SDLP Health spokesperson Conall McDevitt said the minister's statement only confirmed "fears about the DUP lurching towards the further privatisation of our health and social care systems".