Grangemouth, Britain's third largest refinery, has begun shutting down some of its production in anticipation of a two-day walk-out by 1,200 workers on Sunday in a row over pension changes.

The strike could not only force the closure of the site but also BP's Forties pipeline, putting in jeopardy the output of 50 North Sea oilfields. The pipeline delivers almost one third of the UK's daily oil output.

With panic-buying threatening to break out at the pumps, the energy minister, Malcolm Wicks, tried to calm motorists. "[Drivers] might have to be patient," he said. "People will have to be sensible and rational."

But he added: "I cannot guarantee that every garage forecourt will have petrol at that precise moment."

In response, the Scottish Executive announced last night it would coordinate events from an "emergency room" in Edinburgh. John Hutton, the minister for business and enterprise, told the Commons that the situation would be closely monitored.

Grangemouth, near Edinburgh, is unlikely to return to full capacity for up to three weeks. It processes 210,000 barrels of crude oil a day and supplies Scotland, Northern Ireland and parts of northern England, including Northumberland and Cumbria.

Wicks said there was no agreement between the Unite union and Grangemouth's owners, Ineos, about how the Forties pipeline – which he called a "crucial" piece of infrastructure – could be affected. However, it was understood a decision would be taken in the next 24 hours on whether the pipeline will have to be closed.

The offshore oil industry body, Oil and Gas UK, warned that closing the pipeline could cost an estimated £50m a day in lost production, with the Treasury taking half that hit.

Wicks urged both sides to resume talks to resolve the dispute over the closure of Ineos's final salary pension scheme to new workers.

Scotland's first minister, Alex Salmond, said there were enough supplies of petrol and diesel to last well into May.

There was concern that petrol stations may take advantage of the panic created by the possible shortage by profiteering. Motoring organisations warned drivers to make sure they did not get ripped-off after reports that prices at some pumps jumped by up to 5p a litre in the last 48 hours.

However, they advised motorists not to panic-buy as this would only aggravate a fuel shortage. Despite the pleas, supplies at many Edinburgh petrol stations were running low this morning, and one had run dry.

Several filling stations had just two or three pumps open, with queues two or three cars deep. One driver was seen filling up two jerry cans and a tank before paying.

Wicks said: "There are short term stock outs occurring at some filling stations in Scotland, but the petrol industry is confident they can continue to resupply from stocks and imports, even in the event of this strike going ahead.

"This is not a supply issue, it is a logistical issue. What is vital is that Ineos and Unite get back to the negotiating table to sort this dispute out and to avoid any further inconvenience in Scotland."

Downing Street also urged the two sides to get back round the negotiating table to resolve the dispute. "We believe that this is a dispute that should be resolved," a No 10 spokeswoman said. "We are encouraging both sides to get round the table and bring about a resolution based on common sense."

A mass meeting will be held at Grangemouth today addressed by Tony Woodley, the joint general secretary of Unite, who will make clear that the union intends to "steadfastly support" the workers involved in the dispute.

He repeated the union's first warning that the dispute could escalate unless the deadlock over pensions was resolved. "We understand the seriousness of the situation," Woodley said. "It is extremely serious - that is why Unite has been behaving responsibly.

"We have made sure the plant and equipment is in a state to start up extremely quickly and we have made sure there is emergency cover for the emergency services." Woodley accused Ineos of "going through the motions" during the two days of peace talks this week at Acas.

Talks to resolve the dispute collapsed on Wednesday evening and a union official said last night he was "pessimistic" about reaching any agreement.

Motorists are not the only ones who could lose out from the strike. James Withers, the chief executive of the National Farmers Union in Scotland, said farmers could face major difficulties if fuel supplies run dry.