The Health Minister apologised to the patients and families affected, with more than 1,000 records of patients seen by Mr O'Brien between January 2019 and June 2020 so far reviewed.
The trust said "clinical concerns" were raised and patients had been recalled in October after the review. It said "a small number" were affected.
Speaking to the Belfast Telegraph outside his Co Tyrone home, Dr O'Brien said: "I welcome the announcement of the minister for a public inquiry into the urological services provided by the Southern Trust, and I very much look forward to participating in it."
So far the care of nine patients has been identified as meeting the threshold for a serious incident, something defined as potentially leading to serious or unintended harm.
Further concerns have been raised about the private work of Mr O'Brien carried out outside the trust.
Mr Swann said he had contacted the consultant's solicitor, asking him to outline how he will ensure that those private patients are alerted to any issues and that their immediate healthcare needs are met.
The Health Minister also informed MLAs that the independent inquiry panel set up in relation to the recall of neurology patients of Dr Michael Watt at the Belfast Trust would be upgraded to a statutory public inquiry, meaning witnesses can be compelled to give evidence.
Dr Watt was at the centre of Northern Ireland's biggest ever patient recall, in 2018, when around 3,000 people were recalled as part of an investigation into his work at Belfast's Royal Victoria Hospital.
But Mr Swann faced criticism from Alliance health spokesperson Paula Bradshaw, who said it should not have taken another patient recall for the independent neurology inquiry to be converted into a full public inquiry.
"Incidents like this constitute a serious breach of public trust in our health service. That is why a public inquiry is the right move and why one is also long overdue into neurology," she added.
"It should not have taken an event of this scale for that to happen with regard to neurology.
"The question many people will have is whether this sort of failure may still be occurring in the Southern Trust or any other trusts."
In relation to the concerns about the clinical practice of Dr O'Brien, Mr Swann told MLAs that to date 1,159 patients' records had been reviewed and 271 patients or families had been contacted by the trust.
"Unfortunately, we are only at the start of what is likely to become a long and detailed investigation," he said.
"As Health Minister, I want to unreservedly apologise to these patients and their families for any upset and distress this has caused.
"I believe this (a public inquiry) is the best way to ensure that the full extent of the concerns are identified and for the patients and families affected to see that these and all relevant issues are pursued in a transparent and independent way."
Stormont Health Minister Robin Swann. (NI Assembly/PA)
Chief Medical Officer Dr Michael McBride described the development as a "very sad day".
"I don't want to pre-empt the outcome of the outgoing investigations, but any time that we let down the public we serve is a time that we hang our heads in shame," he said.
"Without prejudging, we just need to await the outcome of the investigations that are ongoing and, indeed, the public inquiry."
Colm Gildernew, chairman of the Stormont health committee, described the situation as "concerning".
DUP MLA Jonathan Buckley said it would "no doubt cause concern for patients across the Southern Trust".
Upper Bann MP Carla Lockhart added: "Clearly, the trust and the minister have established serious concerns about safety. I would implore the minister also to look at the wider issue of clinical governance. As it stands, it is not robust enough."
Sinn Fein MLA John O'Dowd described the minister's announcements as probably the most disturbing he had heard.
"There is a problem within the culture of the health service. Consultants have too much power," he said.
Robin Swann said he "unfortunately recognised" what Mr O'Dowd had said.