Update protobuf to 2.5 on Centos 6:

$ cd /usr/local/src/
$ wget https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.gz
$ tar xvf protobuf-2.5.0.tar.gz
$ cd protobuf-2.5.0
$ ./autogen.sh
$ ./configure --prefix=/usr
$ make
$ make install
$ protoc --version

Install protobuf for java

$ cd java
$ mvn install
$ mvn package

You should be good to go.

To enable you to install different versions of protobuf, install stow then change ./configure --prefix=/usr to ./configure --prefix=/usr/local/stow/protobuf-2.5.0

Then link protobuf into your system with stow:

$ cd /usr/local/stow
$ stow protobuf-2.5.0

Note: stow uses /usr/local/bin by default. Make sure thats in your $PATH

To unlink that version of protobuf,

$ stow -D protobuf-2.5.0