Officials said the website - irsofficersonline.Gov.In - was hacked late evening and a message posted on the wall of the portal read "Pak Cyber Thunders. Hacked by Pak MOnster!"
The website, they said, has been rendered inaccessible as of now.
A screen grab of the hacked site read: "shame on your security. Your site is hacked is because of your high security!" along with messages like "Pakistan Zindabad".
Incidentally, the same portal was hacked in February last year and messages such as "Pakistan Zindabad" and "we are team Pak cyber attacker" were posted on it.
They said the technical team handling the website has sent a report in this regard to the Computer Emergency Response Team of India (CERT-In), which is the nodal agency to combat hacking, phishing and to fortify defences of the Indian internet domain.
Officials said a security audit will be undertaken of the website, adding no sensitive or secret information was uploaded on the universal resource locator (URL) of the IRS community working in the I-T department.