Answer: As in the clauses: Article 1, Section 2, Clause 3:
“Representatives and direct Taxes shall be apportioned among the several States which may be included within this Union, according to their respective Numbers, which shall be determined by adding to the whole Number of free Persons, including those bound to Service for a Term of Years, and excluding Indians not taxed, three fifths of all other Persons.”
They counted slaves as less than one person, the "other person" are slaves. The "excluding Indians not taxed" part, means that they were considered part of US only if they paid the taxes.
