Hoopers Inlet is likely to attract duck-shooters as the season begins today.
It is the second year in a row sea lions have visited the site. Last year, the animals had mostly left by the time the shooting season started.
This year, at least eight mother-and-pup pairs are still in the area.
Mr Fyfe said rather than tell hunters not to go there, the department would monitor the impact shooting had on the animals.
"It's something that we want to gather more information on. It's not intensive shooting, so we don't want to make it too big of an issue if it doesn't need to be."
One option was shooters waiting a few extra weeks next year from the start of the season to allow the sea lions to move on.
Hunters needed to be wary of their presence, Mr Fyfe said.
"Loud noises can upset sea lions and they may panic or behave unpredictably if disturbed.
"This site is definitely emerging as a preferred creche area for sea lions and there are very few other areas like it on the coast."
Hunters should not fire within 100m of a sea lion, not fire in the direction of the animals and make sure dogs had permits and were under control.
Otago Fish & Game officer Morgan Trotter said it was pleased with how the hunters showed the animals respect last season.
"We had a couple of hunters decide they don't want to disturb them, so found another place."
Making hunters wait two weeks after the start of duck-shooting season next year would be "quite manageable", he said.
"We are dealing with an endangered sea mammal and a small number of hunters who we could help relocate to another location for that time."
