Is it possible for MPP students to apply for an econ PhD position?
As you might guess, it is more common for a MPP student to apply to a Public Policy PhD vs a Econ PhD. However, you may be a candidate for the Econ PhD if you work the opportunities at Harris.

Like other PhD programs, Econ programs are looking for students who will be successful Economics researchers. You should try to get research experience at Harris and take the most quantitative classes possible. You may also need to take some advanced Math or Econ courses. 

The best way to prepare is to talk to faculty at Harris. You will especially want to discuss the situation with faculty who have PhDs in Economics.