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Government whistleblowers also have claimed that Mr. Mayorkas improperly aided the investor visa application process for a company associated with Virginia Gov.-elect Terry McAuliffe. During a hearing in July, Mr. Mayorkas denied doing so, and Mr. Carper said Wednesday that the author of that decision insisted that Mr. Mayorkas did not influence his deliberations.

Nevertheless, the DHS inspector general’s office is in the middle of probing the claim. Mr. Carper said that while the investigation likely wouldn’t be completed for months, an update last week from a staffer has found no evidence of criminal wrongdoing of anyone at DHS, including Mr. Mayorkas.

Sen. Jon Tester, Montana Democrat, pointed out that any number of people make accusations all the time and that at some point investigators need to deliver. But he also suggested that the program itself may have to be ended if the issues Mr. Coburn alluded to aren’t resolved.

“The EB-5 program may be something we need to work on and do away with, if it’s a problem,” Mr. Tester said.

But David North, a policy analyst with the Center for Immigration Studies, said the program is bad idea and apart from that said Homeland Security is not the right agency to run it. He said DHS is in “over its head” when it comes to investigating financial wrongdoing.

“This is not in the Department of Commerce, the Small Business Administration or Treasury,” said Mr. North, whose group favors less immigration in the U.S. “If you wanted to find out what the climate was at the South Pole, you wouldn’t call the Marines. The Marines are very good at what they do, but that’s not really their thing.”

It appears some of those issues are being addressed, Mr. Carper said.

“It’s not always pleasant for people to hear they’re not doing a very good job or that their skill set might be a better fit elsewhere,” Mr. Carper said. “At the end of the day, though, Director Mayorkas made the difficult — and sometimes unpopular — decisions that he felt were needed to improve this program and move his agency forward.”

For the moment, Congress reauthorized the program, first passed in 1990, for another three years in 2012. But under the immigration bill approved earlier this year by the Senate, the Regional Center program would be permanently authorized.

Sen. Patrick J. Leahy, Vermont Democrat, also introduced an amendment that would add additional oversight tools to the program, like allowing the secretary of homeland security to bar those who have been liable of financial or other crimes from using the program and to conduct background checks on potential regional center managers.

“Those who want to see these reforms enacted should join me in calling on the House to take up the Senate-passed comprehensive immigration bill,” said Mr. Leahy, who also applauded Wednesday’s committee approval of Mr. Mayorkas.

“This nomination deserves consideration by all senators, and that consideration should not be delayed by a highly questionable investigation by the Department of Homeland Security’s office of inspector general,” Mr. Leahy said. “In my view, this flawed investigation does not merit the delay of Director Mayorkas‘ confirmation process.”

Mr. Coburn said it would be a disservice to Mr. Mayorkas, DHS and the Senate to advance the nomination while an active investigation is ongoing.

“If we confirm Mr. Mayorkas under a cloud, we haven’t helped him; we haven’t helped the Department of Homeland Security,” Mr. Coburn said, repeatedly stressing that no criminal wrongdoing has been found but that wrongdoing still could be uncovered. “My hope is that he gets a totally clean bill of health.”

Without a bipartisan vote, Mr. Coburn said, “we will be sending the wrong message to all DHS employees.”

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