Parent group Sequana said the move was a result of a drop in volume in the fine paper market, which has been "particularly sharp" since the beginning of 2009.
Sylvie Noqué, director of communications at Sequana, said the decline had especially been felt in the UK market.
"In order to adapt to the context of volume decline, the group has taken measures to reduce production capacity by moving from a five shift to a four shift," she said.
"Following a consultation period with trade unions and affected employees, an agreement has been reached to move from a five shift to a four shift. This has also resulted in the redundancy of 48 positions at the Aberdeen-based mill."
Unite national officer Peter Ellis said the paper market had experienced a significant rise in the number of redundancies over the past few months.
He said: "Arjowiggins and parent Sequana are looking at saving money. The redundancies here will affect around 10% of the workforce."
In November last year, Arjowiggins proposed the closure of its Dartford plant in Kent, affecting 127 jobs in total. The mill has since closed.
The moves are part of the company's plans to streamline its divisions, which also includes cutting capacity at some of its other European plants.
The Stoneywood mill produces products including Arjowiggins' global brand Conqueror, Curious Papers, Curious Metallics and Impressions ranges.
THIS ARTICLE HAS BEEN UPDATED TO REFLECT THE FACT THAT THE COMPANY HAS SWITCHED TO FOUR SHIFTS FROM FIVE AND NOT FOUR DAY OPERATIONS FROM FIVE DAYS,