The company had warned up to 60 jobs were at risk when it entered a formal 30-day consultation period on July 25.
However, a range of other cost-cutting measures are now being planned to reduce the number of compulsory redundancies.
Michael Hunter, the company's production director, said: "We are currently estimating around 46 job losses, although that number may change as we are still in the consultation period.
"We are proposing a significant reduction in shift working production and overtime work to help make savings.
"In addition, we will be losing one or two through natural wastage in management and administration that we will not be replacing in the near future," he said.
The company is feeling the full impact of the credit crunch and the rapid and severe downturn in the construction industry.
It has suffered a large drop in demand for the timber windows and doors it manufactures at its Ord Road factory and forecasts a reduction in volumes for the rest of the year.
At the same time, bosses say massive rises in electricity costs and the steep increase in distribution expenses caused by the oil price hike have added substantial additional costs onto the business.
Union representatives said they had been expecting a downturn in business but not on a scale that would lead to such large job losses.
"We are looking to notify everyone by the end of this week who is going to be at risk of losing their jobs," added Mr Hunter.
Management had its first 'brainstorming' session with union representatives on Friday and have pledged to look at other ways of making savings during the final fortnight of the consultation.
"Obviously we are still in constant dialogue with the unions and shop stewards and we will be looking at alternative ways of reducing costs further until the eleventh hour," added Mr Hunter.
Last week, managing director Duncan Forster said he was confident that in the medium-to-long term the company had great prospects but it was essential to get through this current difficult period in good shape first.
Allan Brothers currently employs around 240 people making it Berwick's second biggest employer.
It was established in 1811 and is now part of the INWIDO Group.