The collective's website said it delivered 116,483 meals to 450 schools on Wednesday.
But 9.96% of the meals were not on time, up from 0.04% on Tuesday and 0.26% on Monday.
The late delivery blip followed Tuesday's revelation that the collective's main food provider Libelle had opted for liquidation due to financial problems.
The group's lead contractor, Compass, said it would ensure Libelle's kitchens, which produced about 125,000 meals a day, remained open.
RNZ asked the collective if problems with Libelle's facilities were behind the increase in late deliveries.
The collective's spokesperson Paul Harvey said: "Despite Libelle Group's unexpected liquidation, 90% of meals were still delivered on Wednesday - a testament to the Libelle teams on the ground who stepped up to keep the programme running. This proves the strength of this programme and the people behind it. Our focus remains on returning to full delivery as quickly as possible."
Harvey did not say how many schools were affected and in what regions.
