Under project settings 'C/C++ General->Paths and Symbols' the toolchain sysroot needs to be defined otherwise Eclipse defaults to the host include paths. Something such as ${Sysroot}/usr/include as well as other relevant paths should be defined.
http://git.yoctoproject.org/cgit/cgit.cgi/eclipse-poky-kepler/commit/?id=28a2385605c18826e43d308383ee512bd5e7c5b2