The workers have reportedly gone down with sickness and diarrhoea at the multi million pound venue in the past few days.
The bug, which health officials fear may be the highly infectious norovirus, is so far believed to be limited to 2014 employees. There have been no reports of athletes being affected.
Dr Gillian Penrice, consultant in public health medicine for NHS Greater Glasgow and Clyde, said: "Norovirus is the most common stomach bug in the UK and it is common to see the virus in the community. It's usually mild and generally lasts for 24 hours.
"The symptoms being experienced by these individuals are mild and none of the 12 are giving any cause for concern as a result of the virus.
"We are continuing to monitor the situation closely."
The first of 45,000 athletes have moved into accommodation at the 700 home site at Dalmarnock with the rest due to arrive in the next few days.
Around 30 of Team Scotland 210 athletes were today due to arrive for a flag raising ceremony.
Organiser Glasgow 2014 said it had been made aware of a "small number" of cases among the workforce at the site in Dalmarnock and was investigating.
Residents reporting symptoms have been advised to stay in their room and contact officials for help.
A spokesman for Glasgow 2014 said an advisory message had been sent to people at the village as the virus could be "highly contagious."
Speaking at Glasgow airport where a renovated international arrival area was opened to welcome athletes for the Games, Glasgow 2014 chief executive David Grevemberg said staff are monitoring the situation in the village.
"It's a very isolated group of people, a couple of people in our workforce, and business is operating according to normal," he said.
"In any health and safety situation we always take it very, very seriously but it's an isolated incident, the residents at the village have not been affected and have been well briefed but we'll continue to monitor the situation.
"We work very closely with all the medical authorities, we have a great team there that's aware of the situation and gathering and disseminating information.
"As with any global village of this sort we are reminding people to be diligent in terms of their hygiene and cleanliness."