Fonterra closed its local factory last week citing safety of its about 755 staff after it faced angry protests against its tainted milk products.
The dairy giant was facing two court cases, challenging the safety of its products.
"I am now confident that our people are safe and the business is ready to resume operations and continue selling high quality dairy nutrition to Sri Lankan people," Fonterra Chief Executive Theo Spierings said in a statement.
On Friday, a court in Gampaha lifted a ban on the sale of Fonterra products and the ITI said new shipments of milk were free of any contaminants.
Sri Lanka imported milk and milk products worth USD 307 million in 2012 with the bulk coming from New Zealand and Australia.