It follows the awarding of five gigawatts out of a total of six, to two major offshore wind projects in England.
Six renewable energy projects in Scotland secured a CfD award, including four remote island wind projects and two offshore wind projects.
Mr Wheelhouse said: “On the surface it is of course positive that these six Scottish projects have been successful in their applications – and my congratulations to them for doing so.
“But while some of our island projects have done well, serious questions remain as to whether these will be enough to secure our key objective of transmission links to these islands in the near future.
“I will be speaking with Scottish Southern and Electrity Networks (SSEN) and our island stakeholders shortly to discuss where we go from here, and to reiterate the Scottish Government’s unstinting support for these outcomes.
“I also believe that floating wind, wave and tidal developers must be given the same opportunity to deploy devices at scale and drive down costs. We will continue to press the UK Government to commit to a fairer system that offers early stage technologies the chance to replicate the cost reductions we are seeing in offshore wind.
“The further reduction in the strike price is welcome news for the consumer, but will put further pressure on our supply chain to compete in a global market. It essential that the commitments given in the Offshore Wind Sector Deal are honoured and allowing our supply chain to reap the benefits from this sector.
“And many will see the allocation of five of the six Gigawatts available to just two major wind farm projects as an opportunity unnecessarily missed, and question again why the UK Government has chosen to restrict the outcome in this way.
“I’m calling on the UK Government to review the auction system to be far more expansive so that Scotland can meet our net zero emission commitments, reach our energy decarbonisation goals, and maximise the economic benefits of renewable technologies.
“This is particularly pressing now given the call from the Committee on Climate Change call to grow offshore wind capacity to 75GW by 2050. We cannot hope to achieve that goal without UK Government first accelerating its ambition.”