The dentist, who was suspended earlier this year, has not been practising at the Kelburne Dental Surgery in Paisley, Renfrewshire, since March.
The employee also provided locum Sunday emergency cover at Nithbank Hospital in Dumfries between April 2004 and 2007.
NHS Greater Glasgow and Clyde (NHSGGC) and NHS Dumfries and Galloway said patients had been advised of the "very slight risk" they had been exposed to the virus.
Around 3,000 NHS and private patients registered with the Paisley surgery had been treated by the dentist between January 2004 and March 2013.
Most have been contacted by letter by NHSGGC, but there are about 250 NHS patients and 230 private patients who have not been traced.
Around 10,000 people have been tested and no one has been found to have caught HIV as a result of medical or dental treatment.
NHSGGC confirmed the dentist had been suspended by the General Dental Council (GDC) "and as such their licence to practise has been withdrawn". The health board would not say give the dates of the suspension.
A spokeswoman added: "We became aware of the dentist's HIV status in May this year and subsequently referred the dentist to the General Dental Council."
She said the dentist had not been named to "protect patient confidentiality".
In July, a Kelburne Dental Surgery dentist was hit with an 18-month suspension while the GDC investigated his conduct.
The GDC banned 52-year-old Harry Robertson, from practising until January 22, 2015 after a case against him was presented to its Interim Orders Committee. The committee hears cases which are said to have been brought against registered dentists for the sake of public protection.
Neither the GDC nor NHSGGC would comment on the reasons behind the suspension at the time.
Yesterday, NHSGGC would not confirm whether the suspended dentist was the practitioner at the centre of the new warnings.
Dr Syed Ahmed, consultant in public health medicine at Greater Glasgow and Clyde, said: "It is very rare for HIV to be passed from a healthcare practitioner to a patient because all work follows strict infection-control measures.
"These measures are designed to prevent infections such as HIV being passed between people and through our investigations into this case, we are confident that all appropriate infection-control measures were followed.
"Whilst we therefore think the risk is extremely low, we cannot guarantee that there is no risk, so we have set up a freephone helpline where patients can ask questions and then decide if they want to have an HIV test.
"If anyone has been treated at the Kelburne Dental Surgery and has not received a letter but has concerns, we would ask them to call the helpline number."
Dr Derek Cox, director of public health at NHS Dumfries and Galloway, said: "We have identified that 247 patients were treated by this dentist.
"Of these, we are unable to find addresses for 14."
He said people who feel they may have been missed off the list should get in touch.