Bureau of Land Management officials said they recently found about 400 holes over several miles of the trail, which is listed on the National Register of Historic Places and protected under the Archaeological Resource Protection Act of 1979.
The holes are along wagon ruts made in the 1800s through the dirt and sagebrush by thousands of immigrants heading to Oregon, officials said.
"It is the BLM's responsibility to protect and preserve any sections of the Oregon National Historic Trail under its jurisdiction," said BLM Burley Field Office Archaeologist Suzann Henrikson. "The recent damage to the trail near Burley has resulted in a significant loss of history for the American public."
The BLM is seeking information on who did the digging.
"Although owning a metal detector is not illegal, be aware that using this device on lands under federal management may result in a crime," Henrikson said. "If you sink a shovel in an archaeological site on public land, you could be convicted of a felony."
In Idaho, the Oregon Trail generally followed level ground along the Snake River before entering northeastern Oregon, where immigrants crossed the Blue Mountains.