The National Youth Service (NYS) and Integrated Financial Management System (IFMIS) are among host of government websites that were Monday attacked by an Indonesia hacker group, Kurd Electronic Team.
The portals were attacked in the morning with hackers placing their logo on the landing pages, in a clear indication they have taken control of the site.
All the hacked websites are on servers powered by the Unix-based FreeBSD operating system.
Some of the affected websites included those of the Judicial Service Commission (JSC), the Immigration Department, Kenya Meat Commission, Petroleum Ministry and Refugees Affairs.
The other sites that were attacked includes National Environment Trust Fund, the Department of Planning and the National Development Implementation Technical Committee were also attacked.
By the time this story was published, the ICT Authority had recovered the websites and placed them under maintenance.
ICT Authority CEO Katherine Getao confirmed the incident adding that in the case of IFMIS, it's only the website which was affected but the system was up and running.
"It's true that the websites including IFMIS were attached this morning. The office of the government spokesperson should be able to release the official statement on the matter today (Monday)," said Ms Getao without revealing further details.
The attack comes barely a few years after an Indonesian hacker known as direxer took down over 100 government websites.
The hacker is part of an online Indonesian security forum known as Forum Code Security took down the websites following tutorials from the forum.
The news of the hacking was first exposed on the site code-security.net/archives/114.
The attack also comes barely a few years after the Communications Authority of Kenya (CA) website was also hacked.
CA is the State agency that regulates Internet resources for public and private entities.
CA's website was hacked by a group calling itself AnonPlus that replaced the regulator's homepage with a five-point hackers' manifesto promising to "defend freedom of information, freedom of the people and emancipation of the latter from the oppression of media and those who govern us".
The agency is supposed to protect all government sites from malicious attacks.
However in a statement on Monday evening, Government Spokesperson Cyrus Oguna said that 18 government websites hosted on a single server, had been defaced.
"Government databases and ICT systems, including IFMIS and other critical infrastructure are managed within secure government private network that has requisite security, and remain safe," Mr Oguna said
He, however, said that a team at ICT Authority was working round the clock to restore normalcy on the hacked websites.