Other lines in the region proved more punctual with the Hutt Valley, Kapiti and Johnsonville lines recording 95.3, 95.4 and 93.3 per cent punctuality respectively.
"Punctuality is not as good as on other lines because the distance is significantly longer than other lines, meaning more possibility of delays. Also, the fact that there are so few services running on this line compared to others means that one delay or cancellation has a much greater impact on average figures."
There were no plans to increase the number of services on the line, he said.
Work had improved punctuality with 85 per cent of trains arriving on time from July to October, Mr Gabara said.
"Plus we've changed the operational turnaround time of the first train that leaves Wellington each day at 8.25am. This is now leaving on time much more often than previously and this is having a significant effect on all other services."
It was unclear why patronage had decreased but delays caused by speed restrictions might be one reason, Mr Gabara said.
Overall train patronage across the Wellington region increased 2.5 per cent to 11.6 million trips and punctuality rose to 94.3 per cent.
