Mr Lochhead said: "It is deeply distressing when we hear reports of whales dying, particularly mass stranding incidents such as we saw earlier this month in Fife.
"The reasons why whale strandings take place, be it natural causes or linked to human activities, are not known.
"The initial findings do not point towards any obvious health problems, however I hope that by examining and testing the carcasses, SAC will be able to shed light on this concerning issue."
There are many reasons why whales come close to shore and strand, according to SAC veterinary investigation officer Andrew Brownlow.
"Initial results on the pilot whales suggest most were healthy," he said. "Strandings are sadly not uncommon with social cetacean species, where many animals appear to strand because they follow a sick, lost or panicked individual."