The letters make mention of an "incident" on June 30 where scrap metal lying at the side of the track damaged 19 trains. Auckland Transport chief executive Shane Ellison, writing to Kiwirail chief executive Greg Miller, described the incident as "very concerning".
"The damage severely restricted fleet availability and will come at a considerable cost to rectify the damage to the 19 units".
"While the damage to our assets is troubling, our key concern is that this negligence could have resulted in a serious safety incident," Ellison wrote.
Acting Kiwirail chief executive Todd Moyle said Kiwirail had "apologised at the time for the disruption it caused, and repeat that apology now", and said it treated the incident seriously.
Goff and Ellision also complained that the replacement of 16 turnouts on Auckland's Southern Line would result in weekday peak frequency halving to 20 minutes, at very short notice.
Ellison said Kiwirail needed to develop a better asset management programme to avoid shock restrictions of service in the future.
Issues on the track were having a "severe" impact on customers.
"Many of those in the south travelling on rail are travelling long distances and have limited alternative options.
"Riding a bike or paying for an Uber are unattractive and forcing Aucklanders back to their motor vehicles is counter to the 'climate change', 'travel choice' and productivity outcomes Central Government and Auckland Council is trying to achieve," Ellison wrote.
Kiwirail has subsequently said that, beginning Thursday, the network will be capable of services every 10 minutes on the Southern line "as a result of reprioritisation of materials and resources.
In a separate letter Adrienne Young-Cooper, chair of Auckland Transport, and Daran Ponter, the chair of Greater Wellington regional council, made a joint pitch to Treasury secretary Caralee McLiesh to consider appointing more public transport focused people to fill vacant spots on the Kiwirail board.
The letter said KiwiRail would benefit from having asset management, rail safety, and metro rail operations skills on the board.
Kiwirail has long been criticised for prioritising its freight business over passenger rail services.
Ponter said that the voices of organisations focused on commuter rail were "somewhat lost" when it came to Kiwirail's decision-making, which was focused on freight.
"If we leave it to them they'll prioritise the need for investment based on a freight understanding of rail," Ponter said.
He said Wellington needed decisions on things like who had priority on the tracks, and where to invest in track and electrical upgrades made with passenger rail in mind.
Goff could not be reached for comment, Auckland Transport, Clark and Wood declined to comment.