The state department said a computer failed to run a valid random selection for the annual diversity visa lottery.
More than 19m people entered this year’s lottery, which is intended to diversify the pool of new US arrivals.
The results of a new drawing of names will be posted in July.
Doug Welty, a spokesman for the state department office of inspector general told the BBC the investigation into the error in the computer drawing process “should be fairly quick and to the point”.
“We should go in with a very clear scope of work and come out with results,” he said.
The US diversity visa programme, also known as the green card lottery, began in 1994 as a way to encourage immigration from countries under-represented among new arrivals to the US.
To be eligible, applicants must have a high school education or the equivalent and have two years of experience in a profession.
The programme offers 50,000 visas every year, and recipients are granted permanent resident status and may apply for US citizenship.
In 2009, the top source countries were Ethiopia, Nigeria and Egypt, according to a Congressional research report.
The visas are awarded in what is supposed to be a random selection run by a computer.
But a computer glitch selected more than 90% of those names from people who applied within the first two days of the registration period, a state department official said.
The invalid results were posted to the programme’s website in May.
“They were posted in error,” David Donahue, deputy assistant secretary of state for visa services said last month. “These results are not valid because they did not represent a fair, random selection of entrants as required by US law.”