Do you have a table listing departments for each company?

Assuming there are always 4 depts for each company as in your example:

SELECT counts.company_no, counts.dept_no, counts.count

FROM (

   SELECT dept_no = 1

   UNION SELECT dept_no = 2

   UNION SELECT dept_no = 3

   UNION SELECT dept_no = 4

   ) depts

left join counts on (counts.dept_no = depts.dept_no)

ORDER BY company_no, dept_no