Last night Bloomberg reported finance director Thomas Piquemal had stepped down due to concerns over the project, which is likely to cost £18bn.
In a statement today EDF confirmed the resignation, adding it had provisionally appointed Xavier Girre, currently the chief financial officer of the company's French arm, as Piquemal's replacement.
Chief executive Jean-Bernard Levy said: "Thomas Piquemal told me of his resignation last week, which was made public last night. I regret the haste of his departure.
"With the support of its shareholder, the state, EDF can confirm that it is looking to invest in two reactors at Hinkley Point under the best possible financial conditions for the group, with the objective of making a final investment decision in the near future."
Piquemal is the second EDF executive to step down this year, after the project's director, Christopher Bakken, left his role in February.
The site has been plagued by delays and controversy as costs mounted. In January the company delayed a crucial board meeting as it struggled to find financing for the project.
EDF has a 66.5 per cent stake in Hinkley Point, after China's state nuclear firm CGN bought a 33.5 per cent stake in October last year.
Once the project is completed, it's expected to provide low carbon electricity to six million homes for 60 years, creating 25,000 jobs.
It is expected to begin generating power in 2025.