I had the same problem. Changing the eclipse.ini file as mentioned by #LuteceTheCrab seems to work only when eclipse is launched from the command prompt. However the unity launcher doesn't seem to respect the configuration in the eclipse.ini file.
Upon reading the eclipse.ini in ~/.local/share/applications directory, I realized that the Exec attribute value is set to absolute parameters.
I had to replace the value of the Exec parameter with the path of the eclipse executable.
Name=Java - Eclipse
Exec=/home/[username]/softwares/eclipse/eclipse /* <- Note this line */
This causes the launcher to launch the executable which picks up the .ini in the same directory.
Don't put /* <- Note this line */ in the .desktop file. I have used it to highlight the line in this response.