Members of Parliament have questioned Waka Kotahi and KiwiRail about disruptions to Te Huia train service in a select committee.
The passenger service between Hamilton and Auckland was restricted for several weeks after safety concerns were raised, and began operating the full service again last week.
During a Transport and Infrastructure Select Committee briefing, Waka Kotahi land transport director Neil Cook confirmed Te Huia was not the only train to report a safety issue on the Auckland network.
"We haven't had [another] prohibition notice issued ... [but] there certainly would have been signal passed at danger events over time, yes."
Green MP Julie Anne Genter pressed him to explain why Te Huia alone faced sanction, saying she was trying to understand why there was a prohibition for the one passenger train service but not similar prohibitions for freight.
"I think maybe the key is in the word similar," Cook replied. "Situations may be similar, they are never the same."
Waka Kotahi required Te Huia to have an operational train safety system to return to the centre of Auckland. At first, Waka Kotahi asked KiwiRail to install a European Train Control System (ETCS), which would have taken at least 12 months to be operational.
They have since agreed KiwiRail can use the Electronic Train Protection (ETP) system, which has been installed on the train locomotive.
National MP Simeon Brown asked KiwiRail chief capital planning and asset development officer David Gordon to clarify whether freight trains going through the city had any safety system.
"There is no requirement on the freights to have ETCS or ETP at the moment," Gordon said.
However, he confirmed KiwiRail had entered into a contract to install ETCS on all freight locomotives which operated on the Auckland network.
Waka Kotahi has not yet responded to requests from RNZ last month on more information about train safety incidents.