WASHINGTON — Lt. Gen. Michael T. Flynn, President-elect Donald J. Trump’s choice for national security adviser, traveled to Moscow about a year after he took charge of the Defense Intelligence Agency to cultivate what he saw as natural allies in the fight against Islamist militants: Russia’s spy agencies.

It was June 2013, a briefly optimistic moment for both the Americans and Russians, and Mr. Flynn hoped to take advantage of it. During the trip, which got almost no attention, he met with the chief of the Russian military intelligence unit known as the G.R.U. — the same agency that has since been implicated in interference in the 2016 presidential election — and held an hourlong discussion with midranking officers at its headquarters.

Relations with Moscow have soured significantly since then, yet Mr. Flynn has grown only more vehement about the need for the United States to cultivate Russia as an ally. He even returned to Moscow in 2015, a year after he was forced into retirement from the Defense Intelligence Agency, to give a paid speech for RT, the Russian English-language news organization, which American intelligence agencies have deemed a propaganda tool in the Russian election-meddling.

During that trip he also tried repeatedly to meet officers at the C.I.A’s station in Moscow — housed inside the American Embassy — to press for closer ties with Russia’s spies. But C.I.A. officers in Moscow, who have an adversarial relationship with Russia, declined to meet with him.

Now, as Mr. Flynn, 58, prepares to play a leading role in setting national security priorities in the Trump White House, his pro-Russian tilt stands in striking opposition to the judgments of the intelligence agencies he will help oversee. In an extraordinary report released last week, the agencies bluntly accused the Russian government of having worked to undermine American democracy and promote the candidacy of Mr. Trump.

The report is likely to renew questions about Mr. Flynn’s avowed eagerness to work with Russia, and his dismissal of concerns about President Vladimir V. Putin, which have at times exceeded even that of Mr. Trump himself. Neither has shown any indication of being swayed by the intelligence report on Russian meddling, and the two will within weeks be in a position to reorder American priorities in favor of closer ties with Moscow.

Any shift toward Moscow would very likely put the new administration in direct conflict with senior military commanders and intelligence officials, as well as powerful Republicans, like Senator John McCain of Arizona, the chairman of the Armed Services Committee. It may also rankle some of Mr. Trump’s own cabinet nominees — Gen. James N. Mattis, his choice for defense secretary, and Representative Mike Pompeo of Kansas, the nominee for C.I.A. director, pushed the Obama administration to take a harder line on Russia.

It appears unlikely they will get that from a Trump White House. Mr. Flynn, who is seen as particularly close to Mr. Trump and will serve as a crucial gatekeeper to the president, has said that building ties with Moscow is a strategic necessity to win what he considers a “world war” against Islamist militants.

“What we both have is a common enemy,” Mr. Flynn said in an interview in October. “The common enemy that we have is radical Islam.”

But Mr. Flynn is not always slavishly pro-Russian. He grouped Russia among the enemies of the United States in his book, “The Field of Fight,” which was published in July. In the October interview, which was conducted after American officials first accused Russia of meddling in the 2016 election, he said, “Do I want Russia to…