NHS Highland's proposal to build a new hospital in Broadford and turn Portree into a smaller "spoke" unit has Scottish government approval.
But Holyrood's petitions committee is to ask Health Secretary Shona Robison to review the decision making process.
This follows MSPs' consideration of a petition opposed to the hospitals plan.
MSPs will write to Ms Robison to seek the review by an independent scrutiny panel.
Islanders in the north and west of Skye say if the redesign goes ahead as planned they will be left with a day clinic at Portree and will have to travel further to access hospital services.
As well as the 4,500-signature petition that was considered by MSPs, GPs at Portree Medical Practice have challenged NHS Highland's proposal.
Ms Robison approved NHS Highland's redesign of hospital provision in February.
The new set-up will serve patients on the island and also Lochalsh and parts of Wester Ross on the mainland.
NHS Highland has defended the appraisal of options carried out by a steering group.
The Scottish Health Council has also said the process was legitimate.
Following the petitions committee decision, NHS Highland said: "We believe that the public consultation we conducted into proposed service redesign for Skye, Lochalsh and south west Ross was robust and fair, and this view has been supported by the Scottish Health Council.
"Indeed, the Scottish Health Council carried out a full and independent review of the process and endorsed it.
"In approving our redesign proposals in February the cabinet secretary for health, wellbeing and sport said she was satisfied that NHS Highland conducted the process in a 'meaningful and inclusive way, providing local people with numerous and reasonable opportunities to express their views'.
"We are, of course, sorry that some people in the north of Skye believe that the redesign is flawed."
People in Skye campaigning against the downgrading of Portree Hospital have won a victory in their fight against the plan.