"As to timing, we were hoping to get this done a couple of weeks ago and we're obviously not there quite yet," Tilden said on Alaska's third-quarter earnings call.
He said issues raised during an ongoing review by the Department of Justice antitrust division are "manageable."
"We are working through that process and we are respectful of that process," Tilden said. "We are very confident that the deal will get done."
"This is a pro-consumer merger of two smaller airlines," Tilden said.
In April, the two carriers announced plans to merge. In June, they promised the Justice Department they would not close the deal until Sept. 30 unless the department concluded its review before then.
On Sept. 26, the carriers agreed to extend that deadline to Monday, Oct. 17.
Alaska has offered $57 a share for Virgin America stock. In late morning trading on Thursday, Virgin shares were trading up 30 cents at $54.45.
On the call, Andrew Harrison, chief commercial officer, said the combined carriers would provide 31 daily flights to the New York area.