The hours-old pup was busy devouring milk from its 6-year-old mother, Gem, and seemingly oblivious to the activity.
Beach users contacted Doc staff after finding the pair on Tomahawk Beach.
Programme manager biodiversity assets David Agnew said it was rare for a sea lion to give birth near a popular beach.
"They usually choose more isolated spots." he said.
The 50 metres of bright orange fence would deter dogs and highlight the pair's position to beach users, while still allowing the mother to leave and get food, Mr Agnew said. He was assisted by biodiversity assets ranger Mel Young.
Warning signs would also be placed at the entrance to the beach, with dogs the main danger for the pair, he said.
In the past, a mother and pup had been moved from Smaills Beach, but ideally Gem and her pup would be left at Tomahawk, as staff did not want to put the animals under further stress.
Doc will reassess the suitability of the site daily and any volunteers interested in helping keep watch over the pair during the next week are invited to contact the department.
New Zealand sea lions are listed as a critically endangered species.
Last week, New Zealand Sea Lion Trust trustee Shaun McConkey filmed a dog attacking a young sea lion at Blackhead beach.
Even the least aggressive dogs can disturb marine animals breeding along Otago's coastline.
Under the Dog Control Act, it is an offence to harass wildlife and penalties include instant fines.
