"Today we can finally reopen our key applications," Maersk said in a statement on Monday.
Two Maersk vessels arrived and departed from Port Chalmers without incident during the past week.
Maersk, which handles one in seven containers shipped globally, said it expected to have all its 1500 applications fully functional within a week.
Maersk said on Friday it expected client-facing operations to return to normal by Monday and was resuming container deliveries at its major ports.
Maersk’s port operator APM Terminals said on Sunday that all terminals had resumed operations and it would continue to increase productivity and available services. The Maasvlakte II terminal in Rotterdam would be able to make import deliveries starting Monday, it said.
"We are humbled by the number of people who have offered their help, and the flexibility shown has been tremendous," it said.