The HSE said at least nine people have died in storage areas since 2002 because of carbon monoxide poisoning.
It said the carbon monoxide was given off by the stored pellets and proved fatal because of the enclosed nature of the storage facilities where oxygen is depleted.
The warning comes as increasing volumes of wood pellets are imported to the UK from North America and Europe to serve the growing biomass sector, with biomass boilers becoming popular in factories, schools, power stations and homes.
Four people have died in Europe when they entered ship cargo holds containing wood pellets, and two others died in storage silos.
Since 2010 there have also been three deaths in domestic wood pellet storage sites, including a man in Ireland who was overcome by carbon monoxide in his 7-tonne pellet storage room.
"Although there have not been any incidents so far in the UK, the use of wood pellets is increasing and awareness of this danger is required," the HSE said.
For full details on the HSE’s safety notice visit www.hse.gov.uk
