Puerto Rican voters endorsed a nonbinding referendum for statehood Sunday, but low turnout suggested that the island’s more than three million inhabitants are split on the best path out of the territory’s economic crisis.

According to early results on a government website, statehood drew 97% of support with more than 90% of votes counted Sunday afternoon, but less than one in four voters participated in the plebiscite as opponents called for a boycott. Polls closed at 3 p.m. Sunday.

The...