Scotland boasts only “modest” reserves of shale gas and oil compared to England, and these may be difficult to access, according to a government-sponsored report on Monday that poured cold water on the idea of the country repeating its North Sea success through fracking for fossil fuels onshore.

But the report studied only a small area of Scotland, including the most heavily populated areas between Glasgow and Edinbugh, and the Firth of Forth, and found that the recoverable amounts of gas and oil from the deposits were as yet unknown – as is still the case in England.

The findings have stoked controversy over the heavily disputed future of oil and gas in the UK, if Scotland should choose independence in its referendum this autumn. Energy security is a key issue in the debate, with pro-independence campaigners claiming an energy-independent future for a Scotland outside the Union – using North Sea gas, oil and renewable energy resources such as wind and tides – while pro-unionists argue that the energy future of the country is closely bound-up with the rest of the UK.

The Midland Valley of Scotland – the populous low-lying central region of Scotland that includes Glasgow and Edinburgh – has an estimated 80 trillion cubic feet (tcf) of shale gas below ground, according to the British Geological Survey in a report published on Tuesday, the third in a series of studies by the organisation to map shale gas and oil reserves across the UK.

Crucially, however, the authors were not able to estimate how much of this will be recoverable. The broad estimate of the resource is much less than the 1,300 tcf posited to be in the Bowland shale in northern England. The UK uses 3tcf of gas each year.

Shale gas and oil have become accessible in the last decade because of advances in the technology of hydraulic fracturing – fracking – that involves blasting dense shale rocks with a high-pressure mixture of water, sand and chemicals, in order to open up tiny fissures that release the microscopic bubbles of gas or oil trapped within. But the process has come under fire as it has been linked with water and air pollution in the US, and escapes of methane, a potent greenhouse gas.

The BGS findings give a small boost to efforts to develop shale gas resources in the UK, which ministers have backed because they say it will promote economic growth and energy security. The prime minister, David Cameron, has said the government is “going all out for shale” and islooking to change trespass laws to make it possible for fracking companies to drill under people’s homes without their permission.

The Scotland survey also found a potential 6bn barrels of shale oil in the area covered, which compares with the 4.45bn best estimate of shale oil reserves in the Sussex Weald, which the BGS also surveyed recently. The Weald survey was seen as disappointing because it concluded “there is unlikely to be any shale-gas potential [in the area, which runs from Salisbury to Tunbridge Wells]”.

Shale oil is viewed as a more difficult proposition than shale gas, because it is dirtier to extract and likely to involve much more disruption to the local population. Protests against drilling have delayed progress in Surrey and Lancashire, and further demonstrations are likely at any future sites.

Michael Fallon, the Tory energy minister, emphasised the benefits of Scotland, England and the rest of the UK pooling fossil fuel resources in order to be able to access unconventional reserves more cheaply.

Only the UK combined had the “broad shoulders” and “taxpayer commitment” to attract the investment in infrastructure needed to tap the resource, he said. “We are inter-dependent. We have a single energy market in the UK and we benefit from Scottish renewables, and when the wind does not blow Scotland benefits from nuclear [power] in England. It is a single inter-connected energy market and it works very well for consumers.”

But the geologists cautioned that there was not enough data yet in Scotland to be sure of how much of the anticipated resource could be profitably extracted. There is much less data on the area in question – the first to be assessed for shale gas and oil in Scotland – than there has been in comparable areas in England, of which two have so far been surveyed. Wells will have to be drilled across the area in order to find out how much can be explored.

The report also left out the potential of coal-bed methane, a different source of natural gas that can be extracted without the need for fracking – it occurs naturally in coal seams, causing explosions and loss of life where coal was exploited in previous decades – and that has been targeted by several companies as an easier alternative to shale gas fracking.

Green groups seized on the BGS findings as evidence that Scotland would not enjoy a new industry on the scale of North Sea oil and gas, which have been a mainstay of the Scottish economy since the 1960s, and therefore should concentrate on the potential of clean technology such as wind.

Lang Banks, director of WWF Scotland, said: “It’s clear that there’s not going to be a shale gas or oil bonanza in Scotland any time soon. While this study should change nothing about Scotland’s aim to decarbonise its power sector and go fully renewable, in the wider interests of tackling climate change, it’s time for Scottish ministers to commit to start leaving some fossil fuels, including shale gas, in the ground.”

But Ken Cronin, chief executive of UKOOG, which represents the onshore oil and gas industry, welcomed the study, saying: “This report will give reassurance to investors who wish to explore for oil and gas onshore in Scotland and adds to the estimates of significant onshore resources which can help replace the UK’s growing dependency on imports and balance the decline of the North Sea. The oil and gas industry has been operating in Scotland since the 19th century and looks forward to continuing to operate safely and with the minimum of environmental impact or many decades to come.”

Scottish energy minister, Fergus Ewing, said: “I note the publication of this British Geological Survey report, which highlights that only relatively modest amounts of shale gas and shale oil are likely to be present in the central belt, only a fraction of which could be realistically recovered. We are taking a balanced, evidence-based approach to the development of unconventional gas, and convened an Expert Scientific Panel on Unconventional Oil and Gas to examine the issue."

He added that Scotland has "huge renewable electricity potential".