The home, situated on the city’s Culmore Road, was closed to new admissions earlier in May after critical inspections by the Regulation and Quality Improvement Authority (RQIA).
Last week, the regulator said the home has now complied with its requirements.
The 81-bed facility cares for people with learning disabilities and dementia.
Dr Bob Brown, the trust’s director of care and older people’s services, told BBC Radio Foyle: “I very much regret and would like to say sorry to families.”
Dr Brown stood by Owen Moor’s decision to admit several patients in August to their short-break unit.
This was done despite being under investigation from the RQIA, who shortly after an inspection issued a closure notice over the unit.
He said the Western Trust was continually assessing the quality of care at Owen Mor and said on balance it was satisfied the short-breaks unit could admit new patients.
“We stand over that decision because we know that unit was providing good quality care and it was a decision we took to support family requests as well,” he said.
In a statement, the care home said: “Owen Mor Nursing Care Centre has consistently expressed its sincere regret over the distress and concern caused to any resident or their family impacted by our failure to meet full compliance with the regulations and have publicly and privately apologised to those affected.
“We are truly sorry for the time it has taken to reinstate our compliance standards.”
It stated the home has employed an external team of experts to review all aspects of care and governance.
The care home said it was working with the RQIA and the Western Trust and if there is an intractable problem then the matter can be referred to the Ombudsman.