ediff-version-control-package is a variable defined in `ediff-init.el'.
Its value is

Version control package used.
Currently, Ediff supports vc.el, rcs.el, pcl-cvs.el, and generic-sc.el. The
standard Emacs interface to RCS, CVS, SCCS, etc., is vc.el. However, some
people find the other two packages more convenient. Set this variable to the
appropriate symbol: `rcs', `pcl-cvs', or `generic-sc' if you so desire.

You can customize this variable.