The transmission charging scheme for power generators has been likened to South Africa’s former apartheid regime by Holyrood’s energy minister.
Fergus Ewing criticised the UK Government over the policy, which results in higher charges being paid when electricity is generated in more remote locations.
ScottishPower said the cost of the fees was one of the reasons behind the closure of the Longannet power station in Fife.
The coal-fired station – which is the largest power station in Scotland and the second largest in the UK – will be shut down on March 31 next year after 46 years of producing power.
Mr Ewing addressed MSPs at Holyrood about the work the Scottish Government is doing to minimise the impact of the closure.
Former first minister Alex Salmond claimed that if the power plant could be moved from Fife to central London, “instead of paying the penalty of £40 million in transmission charges, it would receive a subsidy of £11 million”.
Mr Salmond added that while a “slight modification” is being made to the system to the charges, this is “nothing like what is required to eliminate this clear discrimination against Scottish energy generation”.
Mr Ewing agreed, saying: “We have a system of transmission charge apartheid in the UK where Scotland is on the receiving end of extra charges.”
He told MSPs: “Energy policy remains largely a reserved matter and the Scotland Bill will not radically shift the status quo.
“So, we must suffer the effect of policies designed in Westminster that undermine our own energy objectives to maintain a balanced low carbon energy mix.”
Mr Ewing highlighted the “huge significance” of Longannet, which has the capacity to power two million homes and employs 236 people directly, as well as supporting hundreds of other jobs.
“Facing unfair transmission charges and rising costs of carbon, ScottishPower concluded that electricity production at Longannet is no longer commercially viable,” he said.
“This is deeply regrettable, and in our view unavoidable, and will have far-reaching consequences for the workers, businesses and communities impacted.”
Tory MSP Murdo Fraser claimed the minister had “focused on the transmission charging issues while glossing over a range of other matters, not least this government’s obsession with wind power”.
The Conservative MSP added: “The SNP’s preferred alternative to the current transmission charging regime would, according to Ofgem, add a staggering £8 billion to consumer bills, hitting hardest in Scotland where fuel poverty is already too high.”
But Mr Ewing insisted this was “entirely wrong”.