McCain charged that Boeing executive Patrick Shanahan was ducking questions during his confirmation hearing, particularly over his response in a written statement that he would look into providing military assistance to Ukraine.
"Inexplicably, you responded by saying you'd have to look at the issue," McCain said at Tuesday's hearing. "It's not satisfactory. Mr. Shanahan."
Shanahan responded by telling McCain that he did support providing lethal defensive weapons to Ukraine, but that did not satisfy the Arizona Republican.
"Not a good beginning. Do not do that again Mr. Shanahan, or I will not take your name up for a vote before this committee. Am I perfectly clear?" McCain said.
"Very clear," Shanahan responded.
In a questionnaire submitted to the committee Shanahan argued he needed to look at the issue more closely when confirmed because he did not have access to classified information.
"The provision of lethal defensive equipment as part of our already robust security assistance program is an option I plan to look at closely if I am confirmed," he wrote. "I do not have access to classified assessments of the performance of the Ukrainian and Russian militaries in the course of the conflict, and particularly the impact of the security assistance we have provided thus far. I plan to examine this issue closely."
When McCain moved on to other senators, things didn't improve for Shanahan, as the Arizona senator complained again after Nebraska Republican Sen. Deb Fischer finished her questions.
"Mr. Shanahan, you're not making me happy," McCain said. "I'm not going to sit here and watch you duck every question and expect that everything is going to go smoothly. It's not."
The resistance from McCain is the latest sign of trouble for Defense Secretary Jim Mattis' Pentagon as it attempts to staff up. McCain has complained that the Pentagon has been slow to propose nominees, urging them to send them to the committee so he can confirm them.
But McCain is known to get upset from time to time at confirmation hearings. When former Joint Chiefs Chairman Gen. Martin Dempsey was up for re-nomination in 2013, McCain briefly threatened to hold up his confirmation before relenting.
On Tuesday, McCain also took issue with Shanahan's experience as a former Boeing executive, saying he wasn't thrilled about having someone who came from one of the "big five" defense contractors taking over as the No. 2 at the Pentagon.
"You have been associated for the last I don't know how many years with one of the five corporations that provide 90% of the defensive weaponry, the weaponry to defend this nation," McCain said. "And your answer was well I'd have to look at the issue. That's not good enough Mr. Shanahan."
McCain has a long history of clashing with Boeing, from his investigative efforts over the company's tanker deal with the Air Force more than a decade ago that ultimately sent Boeing executives to prison to his recent fights over Boeing's United Launch Alliance venture that uses Russian-made rocket engines.
At the conclusion of the hearing, McCain said told Shanahan to go back over his questionnaire and resubmit his answers, and that would determine what he did with the nomination.
He also sent a message up the chain of command to Defense Secretary Jim Mattis and the White House that he was not happy with the lack of information they were providing to Congress about actions in Afghanistan, Syria and elsewhere.
"I want to work with this administration, I want to work with this President, work with new secretary of defense, who I happen to be one of the most ardent admirers of," McCain said. "But I have to tell you in a couple of weeks were going to mark up the defense authorization bill. The President has two choices, give us a strategy, or we will put a strategy that we develop into the defense authorization bill. ... I want to give the secretary of defense the team he needs, but I'm not going to give him a team that I think is business as usual over the last eight years."