Getting a Maltese birth certificate for someone who was born in Malta as a Maltese citizen in 1854 might be a problem, because civil registration of births in Malta for Maltese citizens didn't start until 1863.
I can't imagine that the Maltese authorities would have asked you to produce a document which they would know could never have existed. !
Not that is unless you were talking to the office idiot, and in every country, some officials can be very knowledgeable, efficient, and helpful, but also, sometimes some of them can be...welllll. !
Presumably what you're really trying to do is to prove your descent from a Maltese born ancestor in order to be able to acquire Maltese citizenship which would permit you to apply for a Maltese passport, that would also of course give you citizenship of the European Union, if that is you haven't already got that.