I currently reside in Spain (more like stuck so I can't get one from the Civil Guard/Local Police), having left Malta a few months back, when they requested another Criminal Conduct Certificate I explained my current situation to my AFCO and ended up filling in a "Candidate Self Declaration" form, which basically states that I'm not in trouble with any law enforcement agencies.
So far so good, my SC is in the works (again) and I'm currently waiting for a F2F medical... Maybe talk to your AFCO about a self declaration?
Edit:
"I went to both the guardia civil and local but both refused and said that it must be done online but offered no further assistance"
I missed that post, mine can probably be ignored.