I guess we're splitting hairs on a tangent here, but what you're talking about is really a distinction between full-time and part-time employees, not between permanent and contract employees.
Two counter-examples of contract employees making more than permanent employees:
- I was recently offered a job at a Japanese financial institution on a fixed-term contract. I was told that they had two groups of employees -- one group of permanent employees who were on a fixed (presumably union-negotiated) pay scale, and another group of contract employees who were paid above the scale but subject to individual re-negotiation each year depending on performance. (I also heard of a similar system at at least one of their competitors.)
- A relative of mine was working at a gym for some time as a contract employee (an entry-level job, but on a full-time basis with social insurance). After three years, she was offered a permanent position, but with a significant pay cut on the basis that she was getting better security.
The link you have posted describe the definition of “contract employee” under Japanese Labor Law. However, it does not say anything about the eligibility of 厚生年金 (government pension plan).
That link was more aimed at your comments about lack of vacation, sick days, etc.