You may want to generate only one of the reports, but not the other. To do this you can use the <reportSets> feature within your POM. Below is the default configuration for the plugin. To disable one of the reports, just copy the <reportSets> element below to your POM and remove the <report> you don't want to generate.
<project> ... <reporting> <plugins> <plugin> <artifactId>maven-pmd-plugin</artifactId> <version>2.5</version> <reportSets> <reportSet> <reports> <report>pmd</report> <report>cpd</report> </reports> </reportSet> </reportSets> </plugin> </plugins> </reporting> ... </project>