Scottish & Southern Energy (SSE) chief executive Ian Marchant claimed proposals for extra Westminster support for nuclear energy could seriously damage wind and wave schemes.
Mr Marchant said the move "could have a negative impact on renewables".
He backed a new generation of nuclear power stations, but said state support was unnecessary. SSE, which operates hydro and wind power schemes along with gas- and coal-fired power stations, said: "We don't think nuclear needs any more support."
The UK government has proposed a new system for incentivising power plants with low carbon emissions, such as nuclear.
It would benefit generators that provided constant supplies of electricity, such as nuclear, at the expense of intermittent suppliers such as wind farms.
Mr Marchant said such an approach "potentially just damages the market's disciplines and could have a negative impact on renewables".
He said: "If you design your whole market around getting nuclear built, you risk damaging the way the market operates."
The Scottish Government said Mr Marchant's worries chimed with First Minister Alex Salmond's own concerns about funding for nuclear power.
A spokesman said: "We welcome SSE's support for our position that there is no place for new nuclear support mechanisms that will favour the bottomless financial pit that is nuclear power at the expense of renewables."
Environmental campaigners WWF also expressed disquiet. WWF Scotland director Dr Richard Dixon, said: "Ian Marchant is absolutely right that the market should not be fixed in favour of nuclear power, especially when this will be at the expense of renewable energy schemes and to the detriment of Scotland. Nuclear power is dirty, dangerous and ridiculously expensive and is simply not needed to keep the lights on.
"Ministers should be taking steps to end our reliance on both nuclear and fossil fuels, not finding ways to fix the market or change the rules in their favour.
"Support for reducing energy demand and boosting clean renewables is the only sensible policy to be following. The whole of the UK should be following Scotland's aim of generating 100 per cent of its electricity from renewables."
EDF Energy, which runs Scotland's two remaining nuclear power stations, at Torness in East Lothian and Hunterston in Ayrshire, said: "We have consistently argued for market arrangements to reward secure capacity and we welcome the (UK] government's proposal to place a value on energy security.
"The government's proposals can work for all low-carbon generation: renewables, fossil fuels with carbon capture and storage, and for new nuclear power. Of these, nuclear represents the most affordable way of decarbonising UK electricity generation."
A Department of Energy and Climate Change spokesman said: "We welcome SSE's contribution to the [UK] government's consultation on the reform of the electricity market and will consider the issues raised."