An audit by Apple found that remote dining rooms and dormitories used by workers did not meet requirements.
Around 250 women who worked at the Foxconn plant were affected by food poisoning, with more than 150 ending up in hospital, local media reported.
Foxconn apologised and said it was investigating the situation.
“We are very sorry for the issue our employees experienced and are taking immediate steps to enhance the facilities and services we provide,” the Taiwanese firm said in a statement.
The factory has been closed since 18 December, when the protests began.
An Apple spokesman said: “Following recent concerns about food safety and accommodation conditions at Foxconn Sriperumbudur, we dispatched independent auditors.
“We found that some of the remote dormitory accommodations and dining rooms being used for employees do not meet our requirements, and we are working with the supplier to ensure a comprehensive set of corrective actions are rapidly implemented.”
The iPhone factory, which is about 25 miles (40km) from Chennai, employs 17,000 people.
The food-poisoning cases and subsequent protests also led the Tamil Nadu state government to ask Foxconn to review its worker facilities.
Last year, Apple had to place another iPhone manufacturing partner on probation after worker riots broke out over unpaid wages at the partner’s factory near Bangalore.