In Ubuntu 12.04, I have jdk7 from sun/oracle installed. When locate jni.h, it prints multiple locations
/usr/lib/jvm/java-6-openjdk-amd64/inclu
Above answers give you a hardcoded path solution. This is bad on so many levels (java version change, OS change, etc).
Cleaner solution is to add:
JAVA_HOME = $(shell dirname $$(readlink -f $$(which java))|sed 's^jre/bin^^')
near the top of your makefile, then add:
-I$(JAVA_HOME)/include
To your include flags.
I am posting this because I ran into the same problem and spent too much time googling for wrong answers (I am building an app on multiple platforms so the build environment needs to be transportable).