While the PMO website was restored, other sites, including that of the Press Information Bureau, remained down.
Officials of the National Informatics Centre (NIC), which hosts the websites, said they were looking into the matter.
The officials said the websites encountered some technical glitches because of which they became inaccessible.
"From evening there has been a glitch. It is being looked into by the National Informatics Centre and the websites which are encountering problems will be restored," a senior official said.
While efforts at reaching the websites of the law, oil and agriculture ministries yielded no results, a message, "the specified URL cannot be found", appeared on the website of the Finance Ministry.
Websites of the information and broadcasting ministry, Department of Telecommunications and the Department of Electronics and Information Technology also remained unavailable.