The hacktivist group's "Operation Justice El Salvador" branch has "tried to attack our website to publicize the private information of internal and external users," the economy ministry said.
According to the AFP report, presidential spokesman David Rivas told reporters that the attack took the form of a distributed denial of service.
The attack comes as no surprise, given that it was preceded by threats: "Anonymous threatened several government websites two weeks ago, including that of the presidency, which on Saturday received at least 30 million hits, saturating the system," Rivas told reporters.
The government temporarily took the site offline to stop the attack, Rivas said, while also fending off attacks on the legislative assembly, the National Civil Police and the ministries of justice and labor.
The move is a drastic one, similar to that taken by Adidas, which has also suffered what it called a "sophisticated, criminal cyber attack" that forced the company to take down multiple sites. Anonymous has not claimed responsibility or been linked to the Adidas attack.
This is far from the first government Anonymous has gone after. The group recently defaced the site of Syria's Ministry of Defense to protest a bloody crackdown on anti-government protesters.
In addition, Anonymous previously has targeted the websites of countries including Algeria, Chile, Colombia, Egypt, Iran, Libya, and New Zealand, taking aim at what the group claims is greed and corruption in these countries.
The organization's Ibero-American wing also recently launched OpsCartel, an operation targeting Mexico's murderous Los Zetas drug cartel and corrupt government officials.
This operation resulted in a bloody backlash, with the deaths of three Anonymous-affiliated bloggers; the abduction and subsequent release of another anti-cartel/corruption protester. Because of this violent retaliation, Anonymous last week switched to safer channels to protect bloggers and then over the weekend canceled the operation entirely.
El Salvador is a likely target, given both the country's history on human rights and Anonymous' human rights campaigns. Amnesty International's roster of human rights abuses in El Salvador include repeated death threats against journalists, thousands of killings and disappearances during the country's 12-year armed conflict, an amnesty law that protects those responsible for the killings, and the murder of two environmental activists who opposed mining projects in the central Cabañas area.
The human rights group also cites the country's refusal to sign human rights agreements as well as its oppression of women when it comes to issues of reproductive choice.Follow @LisaVaas