The report, written by the Scottish Environment Protection Agency (Sepa), reveals that a flawed and potentially leaky gas borehole was planned at Cumbernauld close to exploratory water-wells dug by the makers of Irn-Bru, AG Barr, and the sausage skin manufacturer, Devro. There was also "poor borehole construction" at Canonbie, in Dumfriesshire.
Environmentalists and community groups say the food industry's reputation is under threat from the dash to exploit unconventional gas in Scotland. They are preparing to fight plans, at a public inquiry starting on Tuesday, for the UK's first commercial drilling for coalbed methane in Falkirk and Stirling.
The Sepa report, marked "internal only", was written by experts for its Water and Land Policy and Regulatory Support Group and was released under freedom of information laws. "The construction of deep boreholes presents a high risk to the water environment," it says.
Vertical and horizontal drilling for gas down to 2500m poses a greater danger of pollution than boreholes for water, which are mostly less than 100m deep, it argues. Deep saline waters can contaminate more drinkable upper aquifers "if the borehole is not adequately constructed".
The report also points out that "fracking fluids", which could be used to help extract methane, must "not be allowed to leak into other parts of the groundwater system". No fracking - the hydraulic fracturing of underground rock - is currently proposed in Scotland, though critics fear it will come soon.
The Sepa report discloses "poor borehole construction" planned at Deerdykes near Cumbernauld. The borehole would have been lined with cement only down to 100m and risked contaminating test wells dug in the vicinity by AG Barr and Devro, it suggests.
Both firms said they were no longer planning to use water from the wells. AG Barr said it had tested the water at Deerdykes and, though it was suitable for use as spring water, there was not enough to meet its needs.
"Any potential future drilling activity in the Deerdykes area related to coalbed methane or shale gas exploration will therefore have no impact on the quality of our products," said a Barr spokesman.
A spokeswoman for Devro said: "Devro do not use water extracted from a well and have no plans to do so."
Sepa pointed out that the Deerdykes borehole had not been drilled as planned, and had now been granted a licence aimed at ensuring it would protect human health. The developer, Reach Coal Seam Gas, said it had changed the design of the borehole to follow industry "best practice" guidelines.
According to Sepa, four gas boreholes in Canonbie lacked cement lining between 100m and 400m, potentially allowing contamination of an aquifer. Sepa says it has toughened its regulations, and is requiring current owner, Dart Energy, to take remedial action.
Dart, which acquired the Canonbie boreholes in 2012, is also the developer proposing to exploit coalbed methane in Falkirk and Stirling. "Dart has had constructive discussions with Sepa throughout, and has recently finalised arrangements with Sepa to allow Dart to plug, abandon and reinstate [the Canonbie wells]," said a company spokesman.
Mary Church, head of campaigns at Friends of the Earth Scotland, described the concerns raised by Sepa as serious. She pointed out that a coal gas firm in Australia had last month been fined $1500 for contaminating an aquifer with uranium 20 times higher than safe drinking guidelines.
"Unconventional gas is a novel industry in Scotland, and we could end up being the UK's guinea pigs," she said.
Dr Mark Williams, of Concerned Communities of Falkirk who lives close to one of the planned drill sites, said Sepa was too poorly resourced to ensure water was not polluted.