The Swiss group said in a statement there would be a net-loss of 1,000 jobs at different manufacturing facilities across the wealthy Alpine nation, in Basel, Schweizerhalle, Stein and Locarno.
But it stressed that this included the recently announced build up of a cell and gene therapy manufacturing unit in Stein that was expected to create up to 450 new jobs.
Another 700 jobs would be meanwhile be cut over the same period due to a shift in business functions from Switzerland to other Novartis sites around the world, according to the company, which currently employs some 12,800 people in Switzerland.
In a separate release, the company said it planned to exit its manufacturing site in Grimsby in Britain by the end of 2020.
"Three hundred and ninety-five Novartis employees at the Grimsby site are directly affected by the decision, and additional contactors employed through third parties may also be impacted," the statement said.
Novartis has already announced adjustments in its manufacturing units in Japan, the US, and other countries as part of a strategy announced in 2015 amid an increased emphasis on specialised and personalised medicines over high-volume products.
"We are continuing our efforts to globally transform Novartis into a more efficient, agile organisation that can sustainably innovate and deliver breakthrough medicines to patients," company chief executive Vas Narasimhan said in a statement.
"We will do everything possible to help our associates who might be impacted manage through this difficult transition," he said, stressing that Novartis remained "deeply committed" to its presence in Switzerland.
The company, he said, will continue to have its global headquarters, largest research and development centre, as well as a growing "advanced manufacturing footprint" in the country.
The Employe Suisse union meanwhile described Tuesday's announcement as "a bitter pill" and asked Novartis to reconsider moving so many jobs abroad, insisting there was no guarantee this would cut the company's costs.
As for the Grimsby site, Novartis stressed that it was "an effective, well-running operation," and said it was looking at a range of options for it, including divestment, "which could potentially allow the facility to stay
"We will treat every employee with the utmost respect, sensitivity and fairness during this difficult time," Haseeb Ahmad, Novartis UK Country President, said in the statement.
Following the news, Novartis saw its share price rise 0.9 percent to 82.54 Swiss francs in early afternoon trading, outperforming the overall Swiss stock exchange's main index.