Pasquale Tridico said his INPS agency had received some 339,000 applications for the 600 euro ($655) so far, but that hackers had compromised access to the site.
"In the last few days we have suffered several hacker attacks that produced a major breakdown," Tridico told state broadcaster RAI. "They continued today and we had to close the website."
The government has imposed a nationwide lockdown to try to contain an outbreak of coronavirus that has killed almost 12,500 people in under six weeks.
The restrictions have brought much of the Italian business world to a halt, wreaking havoc with many peoples' livelihoods.
In an initial response to the economic crisis, self-employed or seasonal workers can apply to INPS for the special, 600 euro payout.