"They haven't been mean about it, but the rules have just changed so much," he said.
He said the commission plans to submit a bill that would fix the problem when the Legislature convenes next month.
Also Monday, Walker told lawmakers West Virginia is doing a good job retaining doctors who are trained here.
"West Virginians like to come back to West Virginia," he said.
According to a commission report released Monday, 39 percent of doctors graduating from West Virginia institutions set up their practices in the state.
Walker said many of those doctors stayed in West Virginia to complete their residency training, which usually influences their decision on where to practice.
In 2007, 71 percent of state medical school graduates who also received their residency training in West Virginia decided to stay here, according to the report.
Only 14 percent of West Virginia medical school graduates who completed residencies elsewhere returned to the Mountain State.