That is probably the same problem encountered with the m2clipse plugin : You have to tell eclipse to use the JDK when launching Eclipse. Only setting the JDK/JRE on the Window>Preferences has no effect.
For example add this argument :
C:\eclipse\eclipse.exe -vm C:\Java\jdk1.6.0_20\bin\javaw
Or edit the eclipse.ini file to add the vm argument.
There are plenty of possibilities. Check this link to get the right answer : m2eclipse: Eclipse is running in a JRE, but a JDK is required