Workers at the massive nuclear job downed-tools after not getting paid over the weekend when the site was shut due to heavy snow.
Many workers are not local and stayed near the site rather than returning home.
The protesters are employed by the Kier/BAM Nuttall joint venture carrying out civils work on the site and the action was continuing Wednesday morning.
One operative at the site told the Bridgewater Mercury: “Construction staff are currently taking part in a sit-in strike in the canteen at Hinkley C.
“EDF is refusing to pay the weekend pay even though people stayed local ready to work. There are about 500 of us.”
Asked how long the strike was expected to last, the worker said: “Until they pay us.”
Another worker said: “This is not an organised, union-backed strike. We have withdrawn our labour because we are at the end of our tether.
“A senior manager came out and spoke to us just before 12, asking us to get back to work and was met with a resounding ‘no’.”
Another told the BBC: “We got kicked off site last Thursday because of the snow. We couldn’t go home. We had to report in each day.
“I stayed in digs for four days. I was meant to be on shift Thursday to Sunday, but I’m not being paid for the weekend, just Thursday and Friday.”
A spokesman for EDF said: “The majority of the Hinkley Point C workforce are working as normal today. A smaller number of workers are disputing payments for bad weather and they are being encouraged to return to work.
“Employees who were unable to work at the site during recent bad weather will be paid in line with agreements signed with the trade unions.”
EDF sais the safety of its workforce is paramount and a decision was made to close the site on Thursday ahead of the bad weather.
Work was carried out over the weekend to ensure the site was available for a safe return to work this week.
Peter Hughes, South West Regional Secretary for Unite said: “It is completely unacceptable for Kier/Bam to decide not to pay its workforce while those workers remained available for work during last week’s extreme weather and across the weekend”.
“The current problems at Hinkley were not organised or caused by Unite but the actions of their employers; however the union is currently in intensive negotiations to seek a resolution to the issues with both Kier/Bam and the client EDF.
“Unite understands that workers were told last Thursday during the working day to return to their lodgings.
“The union’s members were due to work the weekend and were available to work; although were instructed not to report for work due to the red weather warnings.
“On their return to site this week they were advised via text that they would not be paid Friday, Saturday and Sunday, the union continues to seek an acceptable and negotiated settlement to these issues”.