It turned out to be a bug with Maven 3.0.3
As a workaround, added maven-jar-plugin to generate manifest file with class path entries and added manifestFile property to maven-ejb-plugin
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-ejb-plugin</artifactId>
<configuration>
<ejbVersion>3.0</ejbVersion>
<archive>
<manifestFile>target/generated-resources/META-INF/MANIFEST.MF</manifestFile>
</archive>
</configuration>