What is the Doctor implying here? Last summer I did an Internship at a Company and after finishing it with a positive review, I received the offer to write my bachelor thesis in cooperation with that company.

After finding a suitable subject (taken from the list of available subjects) I contacted the Doctor that initialy posted the subject.

In his reply he told me that he would be interested in supervising me but he has to decline as he has not enough time and the University (Chair) would not reimburse him on supervising extern thesises.

Finally he re-emphasized that he is interested in the topic, and asked me to inform him when the company would find another contingence 

I struggle to identify what he means by this.
My first impression is that he'd like to be compensated for supervising me by the company.

I don't know whether this is what he is suggesting or whether this would be indecent at all.

I'd like to here another opinion before proceeding.
The word contingency basically means "possibility". He can not supervise you now for the reasons he explained, but there is a possibility that in future he will. I would take it as a polite no.