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The KiwiRail train stopped for about 20 minutes at the Lincoln Rd level crossing from about 9am.
Engineers could be seen inspecting the broken down locomotive, while a long queue of vehicles waited.
Most drivers made a U-turn in a bid to take an alternative route to their destination.
Smoke could be seen coming out of the engine, which "didn't look normal", one witness said.
A small number of "confused" motorists waited for the train to move.
One witness said traffic was initially backed up along Moorhouse Ave and Lincoln Rd for about 1km.