CWP Renewables - the company behind the Boco Rock Wind Farm - said Prime Minister Tony Abbott's directive to stop investment in wind farms was a blow to projects in regional Australia.
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Mr Abbott - who has previously labelled wind farms as "visually awful" and "noisy" - said at the weekend he wanted the Clean Energy Finance Corporation (CEFC) abolished.
"But while it exists, we believe we should be investing in new and emerging technology - certainly not existing wind farms," Mr Abbott told reporters in Darwin on Sunday.
The Prime Minister's statement comes at a crucial time for the second stage of the Boco Rock project at Nimmitabel.
Boco Rock Wind Farm community liaison representative Siobhan Isherwood said stage two was fully approved, shovel ready, and only awaiting financing before construction could start.
Ms Isherwood said that while the government's stance would not directly stall stage two, it would however send a signal to investors that could affect any wind project in Australia.
“The recent resolution of the Renewable Energy Target (RET) negotiations provided renewed bi-partisan support for renewable energy projects," Ms Isherwood said.
"That delivered much needed investor confidence and certainty.
"It sent the message to the rest of the world that Australia is open for business in an industry which has been booming in other countries.”
But now the $10billion CEFC, which invests in a range of clean energy technologies including wind energy, was "under attack", Ms Isherwood said.
"The draft directive that went to the CEFC over the weekend to remove wind energy from that portfolio muddies the waters and re-introduces uncertainty," she said.
"We’ll see this issue develop further, but in the meantime, investment, projects and regional development stall once again."
Ms Isherwood said wind farms were a cost effective, competitive source of clean energy that played a major role in meeting the 2020 RET.
"It is a shame to see these lowest-cost renewable energy projects continue to be undermined," she said.