Hussein Mahdi had previously targeted other Iraqi government websites to air grievances against the authorities, who have now responded in kind with posts on his social media accounts.
"Not caring about the lives of the people is one of the most important reasons for the destruction of this country," Mahdi wrote on the agency's webpage.
He specifically criticised the agency's alleged reliance on Facebook for intelligence information as well as the monitoring of Friday prayers and of Shiite mosques.
The National Security Service has since announced his arrest, saying in a statement that he is accused of "hacking its website and other official sites".
After his detention, a message telling citizens that "the National Security Service is your service" and that "attempting to hack its website is in the interest of the Dawaesh and the enemies of Iraq" appeared on Mahdi's Facebook and Twitter accounts.
"Dawaesh" is a pejorative term for members of the Islamic State jihadist group, the Sunni Muslim extremist organisation that Iraq is battling in the northern city of Mosul and other areas.
An official from the agency said that it posted the messages on Mahdi's social media accounts after confiscating his phone.
But his detention did not have the preventative effect that the agency might have hoped: the websites of the ministries of housing and construction, municipalities, youth and sports and Basra University were subsequently hacked.
"The goal of the hacking is not sabotage" but rather to call for Mahdi's release, posts on the hacked websites said.
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