The employees, who earn just US$300 a month on average, have US$100 taken from their pay packet every month to pay for visa forms, the Nepalese Embassy in Lebanon said.
Lebanese employees at the factory received a salary increase last month, but pay for migrant workers remained the same, despite rising cost of living across the country.
Following failed negotiations on increased wages, 22 Nepalese and 26 Indians went on strike demanding their higher wages and better rights.
Police arrived at the strike on Tuesday, with the factory's owners trying to deport the protest's three leaders – Nepalese Rajandra Kumar, Narayen Dahal and Indian Ravinder Singh.
However, the workers are threatening to leave en masse if the deportation move goes ahead.
"They are saying they want to send the three of them and the rest of them they want to let them work but I don't think the rest of them will accept that. All of them want the same rights – those three are representing them," Priya Subida, a representative of the Nepalese embassy in Lebanon, said