Four people lost their lives at the Hindi trading center in Lamu county, near the scene of attacks in which 65 people were killed last month, the Red Cross said on Twitter.
Nine more people were killed in another attack in the Gamba area of Tana River county.
Officials said a group of 10-15 men struck at Hindi, situated 15 km (9 miles) from the town of Lamu, and close to the town of Mpeketoni, which was nearly destroyed in one of the attacks in June, at about 10 pm on Saturday.
"They went around shooting at people and villages indiscriminately," Abdallah Shahasi, the area chief, told Reuters.
Miiri Njenga, the Lamu county commissioner, said the attackers targeted some government offices and some properties were burnt down.
The Red Cross said three people were taken to hospital with injuries, from both areas, adding another one was reported missing in Gamba.
The Somali militant group al Shabaab, which has carried out a series of attacks in neighboring Kenya, said earlier it had staged an attack on Saturday evening in the coastal area.
The militants attacked the upscale Westgate shopping mall in the capital Nairobi last September, killing 67 people.