Work permit question (Istanbul)

I shall be working as a Project Coordinator on an EU funded project here in Turkey. There seems to be a little confusion as to whether I need a work permit for this 12 month contract. I will not have an employer as such so cannot get a letter offering me the position in order to get a work permit and also I will not be classed as self employed. Can anyone help me with this, the project has started but the accountant does not want to start paying me in case there are any problems and nobody here seems to know the correct answer???