Moyle said the timing of this could not be avoided or deferred in order to comply with maritime requirements.
"While it's fortunate that this disruption has not coincided with our peak freight season, New Zealand's supply chain faces a challenging few weeks as we manage freight volumes across Cook Strait in a constrained manner," Moyle said.
"We will be able to achieve this but, I'm sorry, we'll be seeking your continued forbearance, co-operation and forward planning to make the best of a difficult situation."
Aratere's link span in Picton has been repaired after a 50-tonne locomotive fell into the harbour and was dramatically recovered.
Full rail operations restarted this afternoon and will operate through until September 19 when the ferry departs for Sydney.
It will run three return services next week to allow KiwiRail's rail customers to move as much freight as possible between now and the ferry's departure across the ditch.
That means from September 20 to September 30, only the Kaitaki ferry will be operating.
Moyle said there will be reduced capacity over this period for road and rail freight.
He asked for the sector's support and understanding during this time.
Capacity allocations will be discussed and confirmed later this week to ensure freight is prioritised, Moyle said.
"Once again, I apologise on behalf of KiwiRail for this unprecedented situation. Our whole team is working hard on every aspect to make the best of a bad situation.
"We will get through it with your assistance and, like you, I look forward to better days ahead. We will do our best to meet your needs in the meantime."
Moyle told the Herald KiwiRail was doing its best to manage an unfortunate situation by giving customers as much advance notice as possible.