Armed police were deployed to two small islands south of Invercargill today after one man allegedly threatened residents and another reportedly shot a seal.

A 27-year-old man, who had access to firearms, was allegedly threatening residents of Potted Head on Big South Cape Island, off the southern tip of Stewart Island, Senior Sergeant Maggie Windle of Invercargill police said.

He was believed to be under the influence of methamphetamine.

The armed offenders squad (AOS) was deployed about 6.15am. The man was arrested and taken to Invercargill for a mental health assessment, she said.

Later in the day a 56-year-old man allegedly shot a seal then assaulted another man on Green Island, near Ruapuki Island, east of the northern end of Stewart Island.

The AOS was deployed about 2pm and the man was arrested and returned to Invercargill, Ms Windle said.

He was being held in custody and was due to appear in Invercargill District Court tomorrow.