P. Daniel Smith said he acted inappropriately but denied that he "touched himself obscenely."
The proposal would essentially end a 30-year effort to reestablish critically endangered American red wolves in the wild.
Yellowstone Superintendent Daniel Wenk hoped to have more time for a bison project and other wildlife work.
The apology comes after an inspector general's investigation.
Daniel Wenk, a highly regarded National Park Service official, hopes to finish key projects, including moving bison to Native American land.
Limitations on oil, gas and mineral exploration under an Obama-era agreement would be removed by a Trump administration amendment.
If finalized, the transfers would represent a second round of abrupt moves within the Interior Department.
The Trump administration wants to sell leases to oil and gas companies as soon as next year.
Americans widely condemned the first proposal to raise entry fees to $70 at some parks. The new $5 increase proposal tracks closer to inflation.
Repairing worn-out infrastructure is expensive, and the Trump administration is getting creative.