I can give you an example for the school I am currently attending (University of Toronto)
Here is the syllabus for the third year EM course in Physics:
"Solving Poisson and Laplace equations via method of images and separation of variables, Multipole expansion for electrostatics, atomic dipoles and polarizability, polarization in dielectrics, Ampere and Biot-Savart laws, multipole expansion in magnetostatics, magnetic dipoles, magnetization in matter, Maxwell’s equations in matter."
Here is the syllabus for the fourth year EM course in Physics:
"Special Relativity, four-vector calculus and relativistic notation, the relativistic Maxwell’s Equations, electromagnetic waves in vacuum and conducting and non-conducting materials, electromagnetic radiation from point charges and systems of charges."
Here is the syllabus for the third year EM course in Engineering Science (EE/EngPhys):
"An introduction to transmission line theory: voltage and current waves, characteristic impedance, reflections from the load and source, transients on the line, Smith’s chart, impedance matching. Fundamentals of electromagnetic theory: Maxwell’s equations, Helmholtz’s theorem, time retarded scalar and vector potentials, gauges, boundary conditions, electric and magnetic fields wave equations and their solutions in lossless and lossy medium. Plane wave propagation, reflection and transmission at boundaries. Constitutive relations and dispersion. Radiating dipole and waveguides."
And here is the syllabus for the third year EM course in EE:
"Voltage and current waves on a general transmission line, reflections from the load and source, transients on the line, and Smith’s chart. Maxwell’s equations, electric and magnetic fields wave equations, boundary conditions, plane wave propagation, reflection and transmission at boundaries, constitutive relations, dispersion, polarization; Poynting vector; waveguides. "
*note that there is no 4th year EE pure EM courses
So if you notice, there is a heavy emphasis on transmission line theory and waveguides in engineering disciplines, which makes sense. Physics usually offers a much more theoretical approach, whereas engineering is much more applied. So there is a difference. Unless you want to do pure theory in graduate school, you should be fine taking either version of the course.
That said, it differs a lot between schools and professors also. Often the syllabi include things which are never even close to being covered due to time constraints. Most often the biggest differences between the courses are the things that get left toward the end, ie. the specialties such as applications and whatnot. Other than that EM will always be EM no matter what way you slice it.
