To do so, just add in the xml file of your report those following lines
<property name="net.sf.jasperreports.export.pdf.encrypted" value="True"/> <property name="net.sf.jasperreports.export.pdf.128.bit.key" value="True"/> <property name="net.sf.jasperreports.export.pdf.user.password" value="mySuperPass"/> <property name="net.sf.jasperreports.export.pdf.owner.password" value="mySuperPass"/>
JasperServer Community 6.0.1
Jaspersoft Studio 6.0.1