One way is to create an Automated Action that is triggered to run when you create and update Contacts:

You may need to install the Automated Action Rules module (if it isn't already installed).

Create a new Automated Action that works on the res.partner (Contact) model.

• Action To Do is Execute Python Code

• Trigger Condition is On Creation and Update
  

• Code is:

if not record.ref:  
  raise Warning("Account Number can't be blank!")  
else:  
  existing_partner = env['res.partner'].search([('id','!=',record.id),('ref','=',record.ref)])  
  if existing_partner:    
    raise Warning("You can't have the same Account Number in Odoo twice!\n\nAccount Number: " + \
      record.ref + " is already in Odoo, assigned to:" + existing_partner.name+ ".")

Given these Contacts in the database:

This is the Warning you will get if you try to save a Contact with an already used Internal Reference: