President Anders Besseberg told Reuters he planned to step down pending the outcome of the investigation, which he said was focussed on "doping issues".
The IBU said in a statement that Secretary General Nicole Resch had requested a leave of absence due to the investigation.
"The Austrian Federal Criminal Police executed a property search under warrant, at the International Biathlon Union Headquarters, on Tuesday, the 10th of April, 2018," the IBU said.
"The search is linked to the investigation focusing on IBU President Anders Besseberg and IBU Secretary General Nicole Resch."
Besseberg told Reuters the investigation focused on doping.
"It is related to some doping issues, that we have not have not been following up on suspicions blood samples and such matters," Besseberg said.
The Norwegian said the IBU Executive Board would be having a conference call later on Wednesday in which he would not be taking part. He said the best way forward would be for him to step down from his role pending the outcome of the investigation.
"I personally will plan to lay down the presidency. Personally I think this is the right thing to do."
He said he expected this also to be the decision of the Executive Board during their conference call.
The IBU said it was "fully cooperating with the investigation and the office remains operational during normal business hours."
"The IBU Executive Board is taking the matter extremely seriously and continues to be committed to operating under the highest standards of good governance and transparency," it said.
The IBU was recently in the spotlight after it went ahead with the season-ending World Cup in Russia in March despite the country's doping scandal and several nations, including the United States and Canada, refusing to send athletes.
(Reporting by Karolos Grohmann; Editing by Ken Ferris and Toby Davis)
