Prof Keith Muir, of Glasgow University, said the results were "not what we would have expected" from the group of patients who had previously shown no indications of their conditions improving.
The trial involved injecting stem cells directly into the damaged parts of the patients' brains, with the hope that they would turn into healthy tissue or "kick-start" the body's own repair processes.
Frank Marsh, 80, one of the nine patients taking part in the trial at Glasgow's Southern General Hospital, told the BBC he had seen improvements in the use of his left hand.
"I can grip certain things that I never gripped before, like the hand rail at the baths, with my left hand as well as my right," he said."It still feels fairly weak and it's still a wee bit difficult to co-ordinate but it's much better than it was."He added: "I'd like to get back to playing my piano."
His wife Claire said: "He had reached a plateau and wasn't really improving [after his stroke]. But following the operation he is able to do things he couldn't do before, such as make coffee, dressing, and holding on to things."
The study involved patients who suffered strokes some time ago and had shown no signs of making any further spontaneous improvement.
Prof Muir said the results were "at the present time not what we would have expected in this group but far from being able to say whether it's something specifically related to the cells".
He said: "We know that some of the cells will survive and potentially turn into relevant tissue. We also suspect that a large part of what we do is kick-starting repair processes that are already present in the body.
"So there's probably a mixture of things going on. Quite what it is that's happening in the patients, we won't know for some time to come."
The stem cells were created 10 years ago from one sample of nerve tissue taken from a foetus.
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Glasgow stroke stem cell trial shows promise