The New Zealand Sea Lion Trust offered the reward because its members were "extremely disappointed that there are people who would commit such an act, and we feel that the message needs to be given, loud and clear, that this is not acceptable", a trust spokeswoman said.
Department of Conservation Murihiku operations manager John McCarroll said Doc staff were horrified by the shooting and painful death of the pup in the Catlins estuary last Monday.
He said staff received reports of a distressed sea lion in the Catlins estuary last Monday morning, but when a ranger went out to investigate, they found the young female had died.
"The sea lion had serious injuries to its hindquarters, which look to have been caused by a firearm, and steel shot believed to be from a shotgun cartridge was recovered from the animal."
Doc staff were "appalled" someone had seemingly shot the sea lion and left it to die a slow, painful death, Mr McCarroll said.
It was believed the pup might have been bearing these injuries and suffering for more than a week.
It was still not known where, when or why the sea lion was shot.
Mr McCarroll said the pup had been sent to Massey University for a necropsy to confirm the cause of death.
He also called on people in the community to come forward if they had information about the culprit.
The New Zealand Sea Lion Trust spokeswoman said it was important that we learned to share our spaces with other species and remembered the beaches were not only ours but belonged to all.
"Our sea lions have only recently returned to the mainland of New Zealand after a long absence.
"They are charismatic and curious animals that will sometimes approach people, making them particularly vulnerable to anyone that might intend them harm.
"The loss of this young female sea lion is another blow to a small, establishing population that has already experienced low pup survival over the last couple of years," she said.
It was especially frustrating that it was a female that began life in such a unique way, 60km up the Clutha River.
The pup and her mother, Jade, made headlines in February when they were discovered on a Tuapeka farm, and Doc coastal Otago biodiversity ranger Jim Fyfe said their discovery so far up the Clutha River was "new, unexpected and exciting behaviour" for the species.
He said pregnant females were known to push inland to escape the attention of males at that time of year, but he never thought they would choose a site so far from the sea.
Anyone with information about the shooting is urged to contact the New Zealand Sea Lion Trust at info@sealiontrust.org.nz or the police.
All information will be passed on to the appropriate authorities and anonymity will be respected.
