A multi-million-pound investment with the potential to bring 250 mostly well-paid jobs to the economically disadvantaged rural south of Scotland was hanging in the balance this weekend, after local councillors "flummoxed" development experts by rejecting a routine planning permission extension.

The decision to derail Scotland's first-ever "very large-scale" data farm was made despite officials' recommendation to extend the site's outline planning consent after three years, and despite a Scottish Enterprise (SE) survey identifying the site - at Johnstonbank Farm, near Ecclefechan - as the second-most suitable site for large-scale data storage in Scotland.

In an ironic twist, Johnstonbank was specifically promoted by SE partly because of its "positive" planning status, as well as its high scores for environmental sustainability, connectivity, and security.

A spokesman for developer Scotia Global - which is in partnership with the French multinational Schneider Electric to develop a new type of modular datacentre on the site - said that a "lack of joined-up strategic thinking about strategic investment" in Scotland was forcing it to consider abandoning the project.

The spokesman said: "We have been advised by our local planning consultant that we should take this to an appeal as the grounds for refusing the extension appear to be spurious in several respects in terms of planning law. After this latest setback we also have to consider whether Dumfries and Galloway is the place to invest, or whether we concentrate on the two other sites we own south of the Border."

Labour councillor Archie Dryburgh led the motion to refuse the extension, carried with the support of Conservative, SNP and independent councillors in a 9-7 vote. Dryburgh told the Sunday Herald he had not been made aware of the existence of SE's "recommendation report", commissioned last year from consultant hurleypalmerflatt before voting against the plan, on the grounds that he had opposed it three years previously.

Dryburgh added that, having opposed the successful original application for being inconsistent with the local plan, "it would have been hypocritical to have made a different decision at the recent planning meeting".

He cited local opposition for the project, and took issue with Janice Kay, the area planning manager, who supported the proposal on the grounds that the local plan does not allocate industrial sites, which lie outwith the local plan framework, according to section D9 of the Planning Act.

Dryburgh said: "I do not agree that it was covered by D9. Nothing to date has changed my consistent position since 2010 and just because officers recommend approval does not mean to say that we as a planning committee [have to] agree."

The Scotia Global spokesman said: "Our proposal for the site, which has received welcome support from Scottish Enterprise, would have involved the construction of 80 separate small-scale data centres operated by a variety of firms owned and leased by our technical partners, Schneider Electric. This is a new kind of modular, build-as-you-grow data centre that would put Scotland on the map for this rising global industry.

"Not to go ahead with it means a loss to the local supply chain of £20 million of work already commissioned from local builder Robertson Scotland to supply a total of 800 outer 'shell' sheds. Erecting each of these would have led to £5000 for local labour, a total of £4m, plus £16m for the civil engineering and site preparation: fencing, roads, ducting and everything like that.

"Scotia Global only employs 15 security and maintenance staff, but each of the data centres within the complex when built would be staffed by technicians employed by the data owners … These are skilled jobs that command salaries of upwards of £75,000. If fully built out, the site would employ 240 of these personnel with 80 on site at any one time."

Russell Brown, Labour MP for Dumfries and Galloway, who recently convened an "economic summit" to address the "seismic decline" in one of Scotland's worst-paid labour markets said: "If this application was OK two or three years back, then what is wrong with it now? Unless something significant has changed, either the [councillors] have to have good reason to oppose it, or the applicants should have no problems in winning an appeal."

However, Dumfriesshire, Clydesdale and Tweeddale Conservative MP David Mundell appeared to support the committee's refusal, suggesting that the developers had failed to "work closely with the local council and gain the support of local representatives".

He declined to say whether he was aware of or agreed with the councillors' reasons for rejecting the application.

SE sources privately said they were "flummoxed" and "frustrated" by the decision. However, a spokesman said: "We've been working with Dumfries & Galloway Council and the developer for a number of years and all share a mutual understanding of the potential of the site.

"It is for the council to determine specific planning applications."