Benficas stores will close in 2019 due to the Zika epidemic, as part of a response against the outbreak.
The company said on Wednesday that it had to make a decision on its future in the country, after the number of new cases of the disease surpassed the expected number.
It said it planned to close 10% of the stores and to cut back on staff by 5% in 2019.
The closures are the latest move in a long process to make Benficas stores smaller and more efficient, in an effort to lower costs and to protect against potential health problems.
Benfisa, a regional supermarket chain, is owned by the Benfizio family, who have controlled the business since the 1980s.
The family’s family business has been a key partner in the Portuguese government since the country declared a state of emergency in March.
The closures were the latest steps in Benfis efforts to reduce its footprint and to reduce costs.
In June, it announced it would close two stores, including one in the south of Lisbon, due to a reduction in sales, in response to a new case of the virus.
Benfenas has also announced that it would be reducing its size by 10% from the current size of 6,500 staff.
The announcement came after the company announced that its sales had fallen by 12% in the past year, and it was planning to lay off some staff.