"It would be deeply regrettable if this branch of Swedish industrial culture, with strong skills and research in the country, were to be crushed by short-term interests where tax planning rather than new medicines is the driving factor," the Unionen, Ledarna, and Akademikerföreningen unions said in a letter sent to the Swedish government on Wednesday.
The union represent staff at the Anglo-Swedish firm's sites in Mölndal and Södertälje.
Also on Wednesday, Pfizer head Ian Read criticized the Swedish prime minister for intimating that Pfizer had broken promises to keep Swedish jobs when it took over Pharmacia.
Facing question from British politicians, Read said Pfizer had to scrap a planned research centre in Sweden when the drug meant to be developed there did not get approval. He said Pfizer had not broken its words, instead detailing the circumstances that had changed.
Politicians in the UK and Sweden alike have expressed concern that if Pfizer takes over Astra-Zeneca - which British media often refer to only as a British company - there will be job losses. The lower tax rate in the UK, compared to the US, has also featured heavily in the debate.
On Sunday, Sussex University economic professor Mariana Mazzucato wrote in The Observer that one could compare big drugs to big banks - companies that reap the reward of public money but cares less for said public's well-being.
"What makes this dynamic particularly problematic for the taxpayer is that the knowledge behind (...) Pfizer products – the key to their long-run profits – has been virtually bankrolled by that same taxpayer," wrote Mazzucato, author of The Entrepreneurial State: Debunking Private v Public Sector Myth.
Despite a Pfizer promise to keep 20 percent of its total research staff in Britain for the next five years - with no such pledges made to Sweden - Nobel laureate and Royal Society head Paul Nurse publicly warned British lawmakers that Pfizer's promises were vague and inadequate.
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The British fears appear to echo Swedish experience of the Pfizer take-over of Pharmacia, which the US company has defended in public since the remarks made by Swedish Prime Minister Fredrik Reinfeldt about his worries for the future.
Pfizer told the TT news agency that it had cut 2,700 jobs after taking over Pharmacia in 2009. Today, 500 people work for Pfizer in Sweden. Most of the original 3,300 jobs were in production, with sites having since been taken out of operation or sold.