Lyons will visit a haematologist in Sydney early next week but there are reports his place in Australia's World Cup squad could be in doubt.
Raftery said: "David had experienced some minor swelling in the calf at training earlier in the week but it hadn't settled down as we'd hoped it would.
"After it happened again today we decided to conduct some further investigations.
"There is some element of danger in all cases of DVT (deep vein thrombosis) but in David's case the clot is below the knee, which is not considered as dangerous as having one in the arm or in the leg above the knee."
The injury is another blow to Australia's hopes of a Tri-Nations and Bledisloe Cup double on Saturday.
The Wallabies are already without suspended winger Lote Tuqiri while Julian Huxley was ruled out earlier this week after injuring his thigh in a prank.
Lyons is replaced in the Australia side by Stephen Hoiles, with Mark Chisholm promoted to the bench.