Deputy spokesman Mark Toner said the State Department does "regret the inconvenience to travelers who are waiting for visas as well as their families and US businesses that have been affected by this problem."
He complimented the Consular Affairs Bureau's "exemplary work" in addressing the computer problems and whittling down the visa backlog.
A team of about 100 computer experts had been working to resolve the hardware failure, which emerged at a State Department facility in the United States on June 9.
About 50,000 applications for visas are received daily by US embassies and consulates around the world.
Toner said that the US issued more than 410,000 non-immigrant visas from June 23 through June 29.
"Consular staff around the world worked throughout the weekend to diminish our backlog, the bulk of which has now been cleared," he added.
While the summer vacation time is busy, the system cranks up into overload toward August, when tens of thousands of students begin to flood to US shores.
According to the US Department of Commerce, close to 75 million tourists entered the United States in 2014.
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