Dr Anne McCloskey, a former Aontú councillor, expressed concerns about young people being given the vaccine.
The Health and Social Care Board (HSCB) and Western Urgent Care (WUC), where Dr McCloskey works, are now investigating, the Belfast Telegraph has reported.
Dr McCloskey says she stands by her comments.
In the nine-minute video, posted on Sunday, she made a number of claims including that there is not enough evidence that it is safe for young people to be vaccinated.
Dr McCloskey said she was “distraught” by the number of young people “damaged” by “unlicensed and unapproved” vaccines.
She said many young people have been “coerced, bribed or bullied” into being vaccinated and that vaccines are “malevolent”.
Health chiefs say the risk of becoming ill from Covid is about 90% lower if you’ve been vaccinated.
The largest study of its kind has indicated that younger people gain more protection from being vaccinated than older people.
The HSCB said it has ordered an “urgent investigation” after receiving numerous complaints “from both GP colleagues and members of the public around her behaviour, comments and conflict of interest”.
The board said it “takes a very serious view of this”.
“Patients often turn to GPs as a source of medical advice and GPs must inspire confidence and trust in patients,” the board said.
“We can confirm that the HSCB is carrying out an urgent investigation into the comments/views expressed by Dr McCloskey on social media and WUC is currently progressing with its own separate investigations and internal processes in relation to the matter.”
The board said Dr McCloskey works on a sessional basis for Western Urgent Care, which is the organisation responsible for GP out-of-hours Services in the Western area.
“This means that she does not frequently work for the service,” the board said.
Dr McCloskey, who came out of retirement at the start of the pandemic, said her views have been in the public domain since last March when she first spoke out against lockdowns.
She added that she is not anti-vaccination, but that she is against the “mandatory imposition of vaccines” on young people.
The GP said she intends to speak to the Medical Defence Union and the General Medical Council later on Tuesday in relation to the investigations.
She said she believes the investigations were revealed to the media before she had seen a private email informing her of the move.
In October, last year Dr McCloskey stood down from Derry City and Strabane District Council because of differences of opinion with her party over Stormont’s handling of Covid-19 and the wearing of masks.
She also also stood down as the party’s deputy leader.
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