The Scottish Environmental Protection Agency said the process by which green waste is shredded, laid out in open rows and turned regularly to promote decomposition may "give rise to bioaerosol emissions."
People exposed to the particles have complained of breathing problems, headaches, nausea and fatigue, the Health Protection Agency said.
SEPA said so far there has been a lack of scientific research on the complaints, but stresses it is treating them with concern, Scotsman.com reported Sunday.
Green MSP Patrick Harvie said "more research in this area is welcome as commercial composting has an increasing role to play if we are to become a zero-waste country."
"However, it's important that agencies are properly supported and funded to do this research and SEPA have been handed multimillion pound cuts by the Scottish National Party that will impact on their capacity to protect our environment," he added.
Wisconsin business offering 'therapeutic cuddling' forced to close
Exploding whale video goes viral on Internet