or

The main concern of the agency is abandoned children.

You change the subject of the sentence and thus the verb.

In the case children is the subject it is a plural so you need to use ARE

concern in this case is the noun. It is not used as verb here. (in order to useit as verb u should say The agency is concerned about abandoned children).

children is the subject (“who is the main concern?)

abandoned childre ARE the main concern of the agency, or ,

The problem of abandoned children IS the main concern… In this case problem becomes the subject to say it in an easy way.

However, “The problem of abandoned children is the main concern…” is correct, but there’s no mechanism in English to imply a subject like this.

Abandoned children are the main concern of the agency.

or

The agency’s main concern is abandoned children.

English is perverse that way….

the problems ARE… the problem IS….

simple.