Mr Mather said the wind farm plans needed careful study
The Scottish Government has said it will not rush a verdict on a wind farm inquiry held 16 months ago.
The 48-turbine Fallago Rig proposal in the Borders was the subject of a public hearing in February 2008.
Roxburgh and Berwickshire MSP John Lamont has criticised the timescale and transparency of the process.
Enterprise Minister Jim Mather said MoD information about the scheme was still being awaited and the project required "careful and thorough consideration".
The Fallago Rig inquiry was held early last year and a Scottish Government reporter made her recommendations in August 2008.
However, discussions have been ongoing since then between developers North British Wind Power and the Ministry of Defence about the potential impact on nearby radar.
Mr Lamont raised the issue in the Scottish Parliament to try to establish when a decision would be made.
He was told by Mr Mather that further information was still being awaited from the MoD.
He said: "Once that information is received, all parties who attended the inquiry will be given the opportunity to make representations on any new evidence."
Mr Lamont claimed the "behind closed doors" discussions highlighted a "lack of transparency" in the process.
Mr Mather replied: "I disagree with that fundamentally.
"Our legal advice, and the advice of the director for planning and environmental appeals, supports our actions on handling further evidence post local public inquiry.
"We are looking forward to receiving updates from the MoD and the developer and moving forward to making the final decision."