Tourists who stopped to use the facilities at the campsite chatted to the protesters and were handed anti-1080 fliers as they watched the helicopters take off and land.
Other protesters stationed themselves at the entrance to the popular Blue Pools about 1km away.
Originally planned for last year, the drop was delayed until the start of this year because of unsettled weather and contractors being used on other Doc pest-control programmes.
Doc Central Otago operations manager Mike Tubbs said while the drop did not take place when it had been originally planned there was no real impact on its effectiveness.
Mr Tubbs said people had the right to protest but Doc believed in some situations aerial drops of 1080 were the best way to safeguard New Zealand's threatened native birds against predators such as rats, stoats and possums.
Warning signs were placed at the entrances to walking tracks in the area last week and the shorter tracks near State Highway 6 were temporarily closed while 1080 was dropped close by.
Doc staff were also placed on some of the longer walking tracks to caution trampers and advise them about the drop.
Makarora was the last part of the pest-control programme in the southern South Island, Mr Tubbs said.
Anti-1080 campaigner Dave Fluerty, who came from Kaka Point to protest, said poisoning was indiscriminate and trapping would be much more cost-effective and kill only what was intended to be killed.
Mr Fluerty described himself as a proper conservationist who was concerned only about New Zealand's natural habitat.
"This land here is not rugged; it's not remote. It could very easily be trapped for a fraction of the money which is being spent at your expense."
UK tourists Marian and Mick Goodyear said they had not heard of 1080 before reading the signs and talking to protesters at the entrance to the Blue Pools.
Mr Goodyear said he could understand the protesters' point of view but he and his wife had not been deterred from visiting the pools.
"We have the same discussion back home and it's the same all around the world and I guess you hope the Government and those in charge are taking the most sensible approach to it."
The signs and the protesters did not deter most of the tourists visiting the pools and about 100 people were swimming, sunbathing and sightseeing at the attraction when the Otago Daily Times visited yesterday afternoon.
