Manas Pengsuth told a news conference that he had tried to do his job and fulfill every step required by the law, but had failed due to political conflicts, Daily News online reported.
As a result, he decided on Monday to tender his resignation to the Election Commission
Nakhon Si Thammarat is one of eight provinces where candidate registrations for the Feb 2 election have yet to take place. The others are Chumphon, Surat Thani, Krabi, Trang, Songkhla, Phuket and Phatthalung. Altogether they have 38 constituencies.
The eight southern provinces are all strongholds of the Democrat Party, which is boycotting the Feb 2 poll.
Candidate registration has been uneventful in the rest of the country and in Bangkok, where violent clashes broke out last week during the political party registration phase.
The last day for candidate registrations is Wednesday.
After anti-government protesters in Nakhon Si Thammarat disrupted registration for constituency candidates on Saturday, Mr Manas said he tried to find new registration venues. He contacted several private and state agencies including Nakhon Si Thammarat Rajabhat University and local temples, but none cooperated with him.
"They did not want us to use their places [as registration venues] because they feared subsequent effects," he said. "The private sector, which previously allowed us to use their venues, later refused us."
His decision was also based on the fact that officers in the provincial election committee did not cooperate with him. As well, he said, election directors of nine constituencies had resigned on the grounds that they were confused and could not do their work in such a limited time due to vagueness and uncertainty about electoral regulations and orders.
"I don't want to perform my duty in the midst of social conflict and lack of clarity about the election because this could cause damage to the people and the nation collectively," Mr Manas said.
Reports said four other provincial election commissioners were able to continue their work regularly despite Mr Manas's resignation.