The complete procedure is as follows (this is on Linux, on Windows it should work as well if you change the paths):

Exit Eclipse
Delete the directory ~/.eclipse/org.eclipse.equinox.security
Create a text file containing your master password, e.g.

echo "secret" > ~/.eclipse/master

Add to the very top of eclipse.ini, found in the Eclipse program directory (as two lines, don't combine into one)

/usr/lib64/eclipse/eclipse.ini
  
  -eclipse.password
  /home/user/.eclipse/master

Start Eclipse again.