The NZ Transport Agency says problems plaguing the $630 million Kapiti Expressway just two years after it opened will not affect the road sections to be built in Horowhenua.

The new road, stretching 18 kilometres from McKays Crossing south of Paraparaumu to Peka Peka, north of Waikanae, has been revealed to have construction flaws resulting in leaking issues and much of it needs repairs, with tax payers to foot a hefty part of the bill.

Parts of the expressway began leaking just months after it opened three months ahead of schedule in February 2017, with moisture breaching a seal between the road's base and asphalt causing discolouration and surface issues.

Now the problem has spread and NZTA has begun repair work on 15.8 kilometres of the expressway after having already repaired 8.9km of lanes last year.

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NZTA acting senior manager project delivery Karen Boyt said the total cost of the resurfacing was $25.2m and it was expected to take around six months, although it was weather-dependent.

Taxpayer-funded government department NZTA will pay 56 per cent - about $14.1m of the bill - while the contractor will pay 44 per cent - around $11.1m.

An NZTA spokesperson said the public could be confident that other state highway projects, including through Horowhenua will not experience the same problems.

"Through the challenges we've faced on M2PP, the transport agency and the construction industry have learnt a lot about the local material properties and associated construction methods," the spokesperson said.

"The transport agency has introduced additional quality controls, and our technical experts are working closely with the road designer and contractor to ensure that the design is appropriate for the local conditions and available materials.

"We are confident that we have the right construction processes in place, and the increased level of testing being employed during construction will ensure that we deliver a top quality highway."