The penguin colony hosts nightly viewings where little penguins will come in from the sea and return to their nests.
However, these are regularly sold out, causing large crowds of tourists to gather along the road outside the facility to try to catch a glimpse of the penguins.
Police were called on Monday night to disperse the large crowd gathered on the road.
Oamaru Penguins science and environmental manager Dr Philippa Agnew said the colony employed staff to manage the impact crowds had on the penguins.
"Contrary to what we’re seeing on social media, we are managing to keep people out of penguins’ paths and help them get to their nests.
"Penguins are a very resilient species, so we’ve got that in our favour and our staff are really well trained to know when the penguins are stressed and when they’re not.
"They all could look at a penguin on the street and go ‘this penguin is stressed, I’ll go move these people back’ and they can tell that by the penguins’ behaviour."
Over the past 10 days, they have seen large crowds of more than 100 people gather along the road, she said.
"We know that when we’re super busy and we’re sold out, that there’s naturally going to be spillover of customers that can’t attend the evening viewing outside of our facility.
"We also know that some people who don’t necessarily want to come here are encouraged to go elsewhere along Waterfront Rd to try and see penguins for free."
Dr Agnew said while they did not have any data on the effects the large crowds were having on the penguins, there had not been any serious incidents in which penguins were in danger or injured.
Oamaru Penguins have been working alongside Oamaru police, the Waitaki District Council and the Department of Conservation to manage the issue.
"The solutions are not easy because it’s a public road. We can’t just close the road because we have a restaurant, we have boat owners, we have scouts, we have multiple users in this space.
"We have the support from Doc staff, we’ve been talking to them, we’ve been talking to the police, we have also been talking to council.
"We are quite proactive in looking for solutions in that space."
One way they have managed the crowd numbers is encouraging tourists to visit during the day rather than at night, Oamaru Penguins operation and commercial general manager Cyndi Christensen said.
"The staff have been really proactive in encouraging people who haven’t been able to book the evening viewing to come in and do a day tour and those numbers have skyrocketed."
Oamaru Sergeant Tony Woodbridge said police were aware of the concerns and actively monitoring the situation.
"While the tourists numbers are high, we will have a police presence in and around there where resources allow. It’s more of a preventive measure than anything.
"We want to make sure that our tourists are safe in that area, that there are no dangers or risks around that."
