Chief executive Ralph Findlay made the warning in the wake of the pubs and breweries group announcing the major reduction in numbers and a 30 per cent fall in annual sales due to the coronavirus crisis.
He feels strongly that the hospitality sector has been unfairly singled out in the latest range of restrictions to fight Covid-19.
"Various governments are aiming at the wrong target," he said, but conceded that it was what had been decided and Marston's had just got to get on with dealing with it.
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"The trend towards more and more restrictions made it inevitable that we had to look at headcount. It has been deeply upsetting and it is frustrating for us on a number of levels.
"It is the first time in 20 years we have reduced the headcount in the business which has grown from employing 5,000 to 14,000.
"Most of those people are under the age of 25 and working in places where jobs are hard to come by.
"Equally we just don't see the data that says that pubs are a source of infection.
"Marston's is trying to deal with different rules in Scotland, England and Wales and in different regions in England. It has become really complicated.
"We are not going to be the worst affected in the industry because fortunately we are not significantly represented in city centres.
"The vast majority of our pubs sell food and even in tier three areas we should be able to keep most open, but what that means in terms of confidence in people spending money we now wait to find out."
Mr Findlay said that annual trading for the group had been better than expected and ahead of the wider market and Marston's had made good progress in reducing debt.
The job cuts will take effect over the next two months with the 2,150 affected staff those who are currently still on furlough.
He said: "That doesn't make it any better. We held off the decision until we had clearer information on what financial support would be available to maintain those jobs and the unfortunate truth is that it doesn't work and we have had to act decisively to protect the jobs of the more than 10,000 people that remain with the business."
The brewery boss said Marston's was still a very viable business, adding: "We look forward to when we come out of this and are in a good position to look again at how to grow the business.
"We have to navigate through the next four to five months and it looks like it will be a bumpy ride."
Meanwhile, the announcement that Marston’s is to axe more than 2,000 jobs has led the union Unite to renew its call for the government to give concrete support for the struggling hospitality sector.
Unite, which has about 580 members at Marston’s, mainly working in the breweries at Wolverhampton and Burton upon Trent, is seeking clarification of the impact on its members.
Unite regional officer Rick Coyle said: “This grim news from Marston’s is another nail in the coffin of the struggling hospitality industry and today Unite renews its call for the government to produce a concrete and coherent package of measures to support the sector which is now on life support.
“Thousands of jobs across the UK are depending on such a package being delivered urgently by chancellor Rishi Sunak, otherwise the UK’s hospitality sector will become a waste land.
“Unite’s members at Marston’s are mainly based at the breweries in Wolverhampton and Burton upon Trent and we are seeking urgent clarification from management on what the announcement means for our members producing such iconic brands as Pedigree.
“Unite will be giving maximum support to our members at Marston’s at what is a desperately worrying time for them and their families with Christmas on the horizon.”