His body was found last April, close to a German defensive trench line, by archaeologists checking the battlefield before pipeline excavations started.
The Defence Force believes the soldier was given a hasty burial by his comrades as they pushed up the ridge towards the town, which occupied a strategic position.
Objects found with the remains included belt buckles, a metal shoulder badge with the letters NZR - New Zealand Rifles - and glass iodine capsules. Soldiers were issued with iodine to treat wounds.
David Dewer, second secretary at the New Zealand Embassy in Brussels, said pipeline work had finished.
It was increasingly rare to find remains from the Messines battle, where 700 New Zealanders died in two days of fighting. A memorial in the town records the names of more than 800 New Zealanders as having "no known grave".
The soldier buried last night was the second discovered during the project.
In July 2011, the remains of a soldier from the New Zealand Rifle Brigade were found at the site of a new water treatment station. He was reburied with full military honours at Messines Ridge Cemetery last February.
The two soldiers now lie side by side.
Land under the battlefield has yielded artefacts dating back to Roman times.
A well-preserved German bunker and trench system was uncovered last year near the NZ memorial. Its contents included a pen and ink pot, a Mauser rifle and a loaded British Lee Enfield rifle, wine bottles, medication, tools, ammunition and a cabinet filled with more than a dozen "ready-to-throw" grenades.
Mr Dewer said local communities had given great support to preserving the memories of New Zealand soldiers.
Many people from the town, the Chief of Defence Force, Lieutenant-General Rhys Jones, and New Zealand's Ambassador to Belgium, Paula Wilson, were to attend the reburial ceremony.
