"Production has stopped. This morning, the machines were no longer working and there is also strong mobilisation in the research division," Jean Kunz from Swiss union Unia told Swiss news agency ATS.
The 700 employees are at the site in western Switzerland are hoping to force Novartis to examine alternatives for affected employees.
The Swiss pharmaceutical giant had announced at the end of October that it would slash 760 jobs in Basel and 320 in Nyon.
Staff at Nyon want direct dialogue with the chief executive of Novartis, Joe Jimenez.
"We want to talk to the person who decides," said Kunz.
Novartis has said it would like to "continue its dialogue with the staff" and that Jimenez has asked Armin Zust, who heads Novartis Switzerland, to meet the Nyon-Prangins employees.