All employees were evacuated from the Wockhardt site, which employs around 400 people at Wrexham Industrial Estate, on Wednesday.
The global pharmaceutical and biotechnology company provides fill-and-finish services for the Oxford/AstraZeneca Covid-19 vaccines – the final stage of putting the coronavirus vaccine into vials.
A spokeswoman said: “All production on site has been paused while the investigation is under way.”
But she added that “a few hours is not going to make a huge amount of difference to the production”.
She said she could not give information on quantities of vaccine on site but that production “had been proceeding at pace to meet the Government contract for 100 million vaccine doses”.
Police officers and a bomb disposal unit were called to the scene mid-morning on Wednesday.
A statement from the company said: “The safety of our employees and business continuity remains of paramount importance.”
A spokesman for North Wales Police said: “We are currently dealing with an ongoing incident on the Wrexham Industrial Estate.
“The roads are currently closed and we would ask the public to avoid the area until further notice.”
A spokeswoman for the Ministry of Defence said an explosive ordnance disposal team based in Chester was called out just after 11.30am and was assisting at the scene.
Downing Street is being kept up to date on developments, a Number 10 spokesman said.
Last week, emergency teams were called out to protect supplies vaccine following flooding at the industrial estate.
All “necessary precautions” were taken to prevent disruption to the manufacture of the jab, a Wockhardt spokeswoman said at the time.