A proposal by Lewis WindPower, a joint venture of Amec and British Energy Renewables, for a 181 turbine facility was approved by Western Isles Council in February 2007.
The scheme would have a generating capacity of 651MW and provide up to 20% of Scotland's domestic electricity requirement.
But Lewis WindPower was last week sent a detailed 14 page letter by a Scottish Government official warning that ministers wanted to reject the proposal because of the impact on the protected local environment.
The site is in an European Union designated Special Protection Area.
The letter asked the developer to submit further information or suggestions.
Lewis WindPower project director John Price said it would respond to the Government's letter and admitted changes might be needed.
Referring to the London Array scheme off the Essex coast, Price said: "It was in a designated area and was reduced in size after a similar negotiation process".
He added that the developer remained committed to the project, and had memorandums of understanding already signed with consultant Halcrow and Scottish contractor R J McLeod.