Can a spanish yacht captain work/sail on a charter yacht under the Malta flag

Yes, no problem.

Why do you think he would not be allowed?

YES. provided he has a valid and current Merchant Mariner Document because those are accepted world wide. AmeriKan 6 pack license are NOT MMD is and they do not count. but if you have a DECK OFFICER'S license. you can move from country to country.

not that simple it is.
-it depends on the size of the yacht
>200GT u need to look it up in the Malta regulations for small commercial boats. Further look up the insurance contract. Many insurers r requiring specific qualification and/or certification for captains & engineers.
<500GT Again, the Flag State Malta might allow u to work as captain if u have a Spanish license for the same kind of vessel. But they may also require u to apply for a Maltese license & sit exames for it. You need to look it up in their regulations.
>500GT Master & officers need the corresponding STCW Certificate of Competency (COC) accepted & transferred into a Cert. of equivalent Competency (CEC) by the Maltesian Flag State Authorities. There will be a document on board that defines what number & levels of crew r needed (the minimum safe manning document MSMD)
>3000GT u will need a commercial license & a Maltese CEC.