IPMG has potentially lost millions of dollars of work after Fairfax decided to close two magazines due to "continued challenging advertising markets".
The media giant revealed it would close The Sydney Magazine and The Melbourne Magazine in November.
The decision is a blow for IPMG firm Hannanprint, which has been printing the magazines at its new Warwick Farm supersite.
IPMG's chief executive of print, Craig Dunsford, said the magazine closures were disappointing, but something that happened from time to time.
"As a business we are fortunate to have a broad range of work across many market segments to absorb such publishing decisions. IPMG has a long and successful relationship with Fairfax and we will continue to work with them on other titles," he told ProPrint.
[Exclusive: Warwick Farm feature]
Fairfax said it was still deciding whether to redeploy the 10 staff who work at the two magazines.
However, it confirmed that at least 45 other publishing jobs would go.
There will be 25 redundancies at the Business Media unit, which includes the Australian Financial Review, BRW and Smart Investor as well as the business sections of The Age and Sydney Morning Herald.
There will also be 20 redundancies at News Media and Life Media, which publish The Age, Sydney Morning Herald, Canberra Times, Brisbane Times and WA Today.
The layoffs reflect the difficult economic environment, said the managing director of the Australian Publishing Media division, Allen Williams.
"While we are satisfied with the actions we are taking to address these challenges, we must also find cost reductions across our business," said Williams.
"It’s no secret to anyone in the media business that magazines have been an increasingly challenged platform. The Sydney and Melbourne titles have been great magazines, but it makes commercial sense to make these changes.
"We remain committed to our other newspaper-inserted magazines and have already begun exploring new digital opportunities in the luxury category."
Fairfax posted a net loss of $16.4 million for the 12 months to 30 June 2013, although it recorded an underlying profit of $128 million once $144.5 million of one-off costs were removed.
[LinkedIn: Was Murdoch right to say newspapers are dying?]
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