Houses have been set alight in Hindi, near Mpeketoni, and a police station has been attacked at Gamba.
According to the Kenyan Red Cross, 13 people had been killed in the two incidents.
The Somali militant Islamist group al-Shabab has previously mounted a number of attacks in the region.
However, it was not immediately clear who was responsible for the latest shooting.
Witnesses said about a dozen armed men had appeared in the trading centre in Hindi, Lamu County, late on Saturday evening and opened fire.
“They went around shooting at people and villages indiscriminately,” area chief Abdallah Shahasi told Reuters.
County commissioner Miiri Njenga told the agency some government offices and properties had been burned down.
The Red Cross said another nine people – eight civilians and one police officer – were killed in Gamba, and one person was also missing.
There were few further details of the attacks – the Kenya National Disaster Operation Centre said confirmed the violence and said on Twitter that it was responding.
Attacks in the Lamu area early last month killed at least 60 people, as gunmen descended on hotels and a police station.
The area includes Lamu island, a well-known tourist resort, however, the attacks happened on the mainland, in Lamu County.
Kenya’s President Uhuru Kenyatta has blamed the attacks on political networks, despite al-Shabab claiming responsibility.
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