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Mr. Miller had cited a “mutually agreed-upon holiday pause,” but Mr. Abraham said that no such agreement had been made.

And last week, during an event at which Mr. Biden criticized President Trump for playing down the Russian hacking of the federal government and private companies, Mr. Biden said, “The Defense Department won’t even brief us on many things.” The department responded by calling that claim “patently false.”

After Mr. Trump’s postelection firing of Defense Secretary Mark T. Esper and a purge of the department’s senior leadership, the Pentagon was put under the political control of several Trump loyalists, including Kashyap Patel, Mr. Miller’s chief of staff, who is best known for his efforts to discredit the Russia investigation when he was a Republican congressional aide.

But even as Mr. Biden complained on Monday about a lack of cooperation from some political appointees in the Trump administration, he also offered praise for career federal government employees who have worked with members of his transition. “For some agencies, our teams received exemplary cooperation from the career staff,” he said.

Mr. Biden also offered a downbeat assessment of the toll that four years of Mr. Trump’s presidency had taken on the country’s national security apparatus.

“The truth is, many of the agencies that are critical to our security have incurred enormous damage,” the president-elect said. “Many of them have been hollowed out — in personnel, capacity and in morale.”

Mr. Biden has emphasized a promise to rebuild alliances and restore the United States’ standing in the world, and he has already named most of his top foreign policy and national security officials — though he has yet to announce his choice to lead the C.I.A.