When copying geometry data into PostgreSQL using COPY FROM STDIN it is a good idea to use the PostGIS HEXEWKB format.
Here's how to create HEXEWKB using Java and JTS:
import com.vividsolutions.jts.geom.*;
import com.vividsolutions.jts.io.WKBWriter;
import com.vividsolutions.jts.io.WKTReader;
import com.vividsolutions.jts.io.ByteOrderValues;