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Some fans have expressed their disgust at the bottle-throwing from the terraces and Otago Rugby Football Union stadium and operations manager Coryn Huddy said the incident "had the potential of marring what was a great event for the city and for rugby".
"We are extremely disappointed that bottles were thrown from the terrace.
"It is a shame that the actions of a few people can detract from the game itself.
"If this type of behaviour continues, then the future of test rugby in Dunedin could be jeopardised."
NZRU professional rugby manager Neil Sorensen said such incidents would be considered when tests were allocated for next year.
The union was "very unhappy" with the behaviour of a small number of patrons at Carisbrook "whose actions reflect very badly on our reputation as good hosts, and true rugby supporters, and on our national image internationally".
Dunedin man Nick Phillips watched the game from the Railway Stand.
He said "early on" in the game people in the terraces started throwing bottles at other members of the crowd and at a man who invaded the pitch.
"If someone had done something about people throwing bottles early on, we may not have had this problem.
"The thing that really got me going was when the French team was doing their lap of honour and people were hurling bottles at them.
"It was just wrong."
He saw a couple of members of the French team jump to miss bottles.
He saw police arrest about two people from the terraces, but expected more to be done.
Stephane Dujakovic, a French supporter who lives in Christchurch, went to the game with a group of both New Zealand and French supporters.
After the game he and his friends went to the perimeter fence of the pitch to clap the French team.
He said it should have been a proud moment but instead he was "disgusted" to see "hundreds" of bottles being thrown at the team.
"I have never seen anything like that.
"The bottles were flying and most of them were full."
He said French forward Sebastien Chabal looked "really pissed off" and called back about half the team.
Dujakovic said a solution would be to get rid of the plastic bottles and replace them with plastic cups, which could not be thrown.
Huddy said staff at Carisbrook had taken steps to minimise the risk of items being thrown from the terraces, including introducing plastic bottles.
He said measures would be made to educate the crowd and additional security added.
"But at the end of the day our fans need to act responsibly if we are to continue to host test matches here in Dunedin."
Sorenson said the NZRU would be working with the ORFU to ensure fans were educated that such