A KiwiRail spokesman said the train was delayed for about two hours while the section of track was cleared and the train was assessed.
While cows could be a derailment risk due to their size, in this case the train only sustained superficial damage to the front and to two air hoses.
No other services were impacted and no KiwiRail staff on the train were injured in the incident.
In the past five years there have been 37 stock trespass incidents reported in the Bay of Plenty, of which 19 involved collisions.
The KiwiRail spokesman said it was farmers' responsibility to keep stock from wandering on to the line, just as it was with farms that adjoined a state highway.
"This incident is a reminder for farmers to ensure their stock is adequately secured, for the safety of both the stock, property and other people."