The hacker, who called himself Muhammad Bilal, wrote "Pakistan Zindabad" messages on the site and called for an end to militarised governance in Kashmir.
The hacking comes close on the heels of a claim by Kashmiri separatist leader Syed Ali Shah Geelani that Narendra Modi had sent two emissaries to him.
Muhammad Bilal, the hacker, began his message by saying, "Good Morning Narendra Modi" and went on to raise the Kashmir issue.
The message posted on the site terms freedom of Kashmir as the goal of those who hacked L K Advani s website lkadvani.in.
Meanwhile, L K Advani, who was in Tamil Nadu today campaigning for the party in Vellore, was not aware of the hacking. None of his associates accompanying him or people at his residence knew of the development.