Abseilers rigging cables to support the plastic skin of the Dome suffered from persistent sores on their lips and red, blotchy rashes on their forearms.
The news re-awakens fears about potentially toxic waste on the site, including cyanide and coal tar contamination.
Blood and urine samples from concerned workers employed by sub-contractor Watson Steel at the Greenwich site, in south London, were negative, and a spokeswoman for main contractor John Laing Construction admitted: "We do not know what caused the rashes."
Greenwich Hospital confirmed that it has treated nine cases of "minor injuries" from the site, including a number of people with skin complaints.
Previously a gasworks, the site is one of the most contaminated in London. Other chemicals contractors have removed from the ground include foul lime waste and heavy metals.
Abseiler Jethro Kiernon, 27, of Sheffield, who has been working on the Dome since October, told the Independent on Sunday: "I was relieved to have the blood test. I have no desire to cripple myself by exposing myself to any dangers.
"There was talk before we went on site of the types of toxic soil that we should keep an eye out for. We were working in dry conditions that were making it very dusty and we were very aware of the dust in the air."
The Transport and General Workers Union, which has many members on the project, is also alarmed and planning its own investigation. Bexley and Greenwich Health Authority will meet Greenwich Hospital's healthcare trust on Monday to discuss the issue.
The Health and Safety Executive said it was happy with the construction companies' safety measures. However, Mr Kiernon claimed that Laing had failed to douse the dusty site with enough water before the outbreak of rashes. The company rejected his claim, saying "we have a permanent water douser on the site, which is working effectively". Watson Steel did not want to comment further.
Another abseiler, Andy Scott, said: "There's some pretty bright green stuff that gets dug out."
A spokesman for the New Millennium Experience assured: "The health and safety of all those involved in the construction is of paramount importance."