Defence Minister Nirmala Sitharaman confirmed the attack, but India's cybersecurity czar denied hacking had taken place, saying a "hardware problem" was to blame.
"Action is initiated after the hacking of the MoD (ministry of defence) website. The website shall be restored shortly," Sitharaman said on Twitter.
"Needless to say, every possible step required to prevent any such eventuality in the future will be taken," she added.
The defence ministry website was the first to be affected, with its homepage replaced by a screen showing a chinese character that means "zen".
Soon, other major departments' websites were either "unreachable" or "not found".
The Ministry of Home Affairs website's main page said that the site was offline "due to technical problems".
Gulshan Rai, the national cybersecurity coordinator, contradicted Sitharaman.
"There is no hacking of any nature anywhere in the Defence Ministry website. There is a hardware problem due to which the website is down. It will be up shortly," Rai told the local NDTV news network.
"Due to malfunctioning of storage network system, websites of few ministries (are) down and will be up soon," he added.
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