Scottish ministers are facing challenges to several key policies from a particularly awkward quarter - the Council of Economic Advisers set up by Alex Salmond.

Its most recent meeting featured disagreement on several controversial policies where the SNP has taken uncompromising lines.

The council members have told the First Minister he should seek independent assessment of nuclear energy before ruling it out, warning it may be necessary to meet the demanding long-term targets set by the Holyrood administration for reducing carbon emissions.

There has also been criticism of the SNP government's block on student tuition fees, with calls from the economic expert to require students to make a personal investment in their education.

The Council of Economic Advisers (CEA) annual report is also to feature a report into the SNP's plans for a Scottish Futures Trust as a means of replacing the Private Finance Initiative. That has been used by previous administrations to lever in money to build public sector capital projects such as schools, hospitals and bridges.

The advisers warned ministers need to move quickly to resolve the question marks over their capital funding, stressing the methods they use have to be efficient and direct.

The tensions between SNP policy and expert economic advice became clear in the minutes of the third meeting of the CEA on June 13. The account of it was published on the government website.

In a discussion on carbon emission targets, ministers were urged to lead a more active debate on all energy options and costs, after "a lively and comprehensive debate" about alternative technological options.

The public debate requires "an honest, careful and balanced assessment of the full costs associated with each of the key energy options was required," advisers agreed.

The council, chaired by former Royal Bank of Scotland chairman Sir George Mathewson and including eminent economists, advised Mr Salmond to commission independent, external consultants to assess costs.

This is in line with pressure from business lobbyists, urging SNP ministers to reconsider their block on new nuclear plants as Hunterston and Torness reach the end of their working lives. Whitehall is planning for a new generation of plants in England.

It is not yet decided whether an independent assessment of nuclear will be commissioned, but a source close to Mr Salmond yesterday welcomed the inclusion of nuclear in the debate. He was confident that the data will show how expensive decommissioning has become, citing a Westminster committee report on costs.

The CEA meeting also challenged the SNP block on student fees. The minutes say there was a wide-ranging debate on the links between fees, the level of participation, skills and productivity.

There was general agreement that there is a sharp contrast in the attitude and commitment between those students who pay for their education and those who do not, and the government should look at ways of ensuring students see education as a personal investment. The government source said yesterday that there are no plans to revisit tuition fees.

The CEA minutes also shed light on government thinking on the economic slowdown. Dr Andrew Goudie, chief economic adviser within the civil service, briefed council members and said there were fewer signs of downturn than the rest of the UK, but warned Scotland's big risks lie in declining business and consumer confidence, which could lead to falling sales and employment.