The biopharmaceutical company said it had concluded a period of consultation with the 220 staff who will be affected by the move, initially announced as part of a company-wide reorganization on November 7th, the ATS news agency reported.
The company said it established a social plan for staff unable or unwilling to make the move that goes beyond minimum legal requirements, ATS said.
Shire acknowledged that the potential changes — involving a move from a French-speaking canton to a German-speaking one — would not be easy for the affected employees.
But the company said it reached an agreement with workers to provide help for them and their families.
The Vaud cantonal government had offered to intervene in a bid to persuade Shire to keep its operations in Eysins, located near Nyon.
Two government ministers met with CEO Flemming Ornskov and a further meeting was planned for the end of this week, the canton said.
The government issued a statement stating that since Shire had reached an agreement with its employees the measures it contemplated to aid the company were now being withdrawn.
It said that Shire justified its move to Zug by arguing that the site was closer to airline connections with Boston and Philadelphia, where it has operations, and that the area between Zug and Zurich offered greater opportunities for recruitment.
The canton said that these arguments did not hold water given that Lake Geneva offers “incontestable” advantages in the health sciences field, employing 7,000 people working for 170 companies in the sector.
The issue of taxation was not mentioned either by the company or the canton.
However, the Financial Times, reporting earlier this month on the Shire move, said that Zug “offers extremely low corporate tax rates and has been favoured by many pharmaceutical companies for their European operations, creating a large pool of staff with easy access to international airports”.
In addition to its Eysins base, Shire also lists on its website a Human Genetic Therapies branch elsewhere in the canton of Vaud in Montreux.
Founded in Basingstoke, England more than 30 years ago, Shire bills itself as a company that offers "treatments for neuroscience, rare diseases, gastrointestinal, internal medicine and regenerative medicine".
The firm is undergoing a shakeup under CEO Ornskov, a Danish MD and former Novartis employee who joined the company in April.
This has led to cuts in research jobs and a refocusing of its business.
According to its website, Shire employs around 5,000 people in 29 countries, although its main operations are in the UK, the US and Switzerland.