This video released by Russia's defense ministry shows Russian warships in the Caspian Sea launching cruise missiles on targets in Syria. (Russian Defense Ministry/YouTube)

Among the first clues that Russia was mobilizing for a military offensive in Syria were requests Moscow began making in ­mid-August for permission to cross other countries’ territory with more and larger aircraft.

“We were getting the word the Russians were asking for inordinate overflights,” a senior Obama administration official said, referring to reports from U.S. allies receiving the requests. Russia was seeking clearance for not only cargo planes but also “fighter aircraft and bombers” that Syrian pilots had never been trained to fly, the official said. “It was clear that something pretty big was up.”

But despite that early suspicion — which only intensified as Russia then deployed fighter jets and teams of military advisers — the United States seemed to be caught flat-footed by the barrage of airstrikes that Moscow launched last week.

The attacks pounded Syrian rebels who were trained and armed by the CIA over the past two years but who appeared to get no warning that they were in Russian jets’ crosshairs. The strikes also damaged a fragile U.S. strategy that sustained an additional blow Friday when the Pentagon acknowledged that it was sharply scaling back its effort to build a force to battle the Islamic State, also known as ISIS or ISIL.

The setbacks involved separate programs with distinct missions. One is a covert intelligence effort to aid Syrian rebels trying to oust President Bashar al-Assad; the other is an overt military operation using U.S. air power and aid to other rebel groups on the ground to decimate the Islamic State. But U.S. officials and experts said that in both cases the Obama administration was slow to recognize and respond to signs of trouble that seem abundant in hindsight.

“It seems to me there’s some kind of gap or disconnect between the intelligence side and the policy and operational side” on Syria, said Jeffrey White, a former Defense Intelligence Agency analyst who tracks the Syria conflict at the Washington Institute. Amid Russia’s buildup “we actually saw quite well what was going on — equipment was tracked,” White said, “and then there was some kind of failure to read what the implications of that were.”

The Russian airstrikes followed a series of moves by Russia that signaled a coming offensive, including the extension of a key runway for bombers and military cargo planes. Similarly, the Pentagon’s rebel training program was beset by problems that seemed potentially fatal from the outset, including enormous difficulties drawing recruits to a force set up to fight the Islamic State when most militants’ priority was the ouster of Assad.

White House officials defended their handling of the Russian escalation, saying they moved quickly to warn Moscow against making the conflict worse, beginning with a call from Secretary of State John F. Kerry to his Russian counterpart the first week in September.

Hesitation to take stronger action against the Russian move, others said, stemmed in part from the administration’s belief, based on an interpretation of signs earlier in the year, that Russian President Vladimir Putin was moving toward withdrawing support from Assad and supporting talks that would lead to his departure.

By early September, as Putin was deploying equipment and personnel into Syria, his message was mixed. He was ready to attack “terrorists” in Syria, the Russian leader said in several speeches at the time, while also making clear that he believed the Syrian army was the only ground force capable of defeating them.

With few options to prevent the Russian deployments and concern about risking a wider proxy war, some in the administration proposed taking “more of a wait-and-see attitude” to determine whether Russia would actually attack the Islamic State, said a U.S. official familiar with the Syria discussions. “But when the first Russian strikes were 40 miles away from ISIS territory,” the official said, “there was a completely different view.”

Syrian activists are reporting that Russian jets carried out fresh strikes in Syria’s Idlib and Hama regions to target opposition forces on Oct. 7. (Facebook/Halab Today TV)

The struggle to find a way to respond has become a source of tension within the administration, according to U.S. officials who said CIA Director John Brennan has voiced frustration with U.S. inaction as fighters trained and armed by the agency at secret camps in Jordan over the past two years face a Russian assault.

The CIA declined to comment on any aspect of its role in Syria.

Reports indicate that CIA-trained groups have sustained a small number of casualties and have been urged to avoid moves that would expose them to Russian aircraft. One U.S. official who is familiar with the CIA program — and who like other officials spoke on the condition of anonymity to discuss intelligence matters — said the attacks have galvanized some of the agency-equipped units. “Now they get to fight the Russians,” the official said. “This improves morale.”

Numerous videos posted online in recent days appear to depict fighters armed with antitank weapons celebrating after destroying Russian-made tanks.

Even so, U.S. intelligence officials said Russia’s intervention is likely to extend Assad’s hold on power and prolong the conflict in Syria, putting additional strain on a U.S.-led coalition that includes Saudi Arabia, Qatar and the United Arab Emirates.

Brennan departed for the Middle East last week as the Russian strikes intensified. U.S. officials said that the trip was previously planned and not related to the bombings but acknowledged that his discussions centered on Syria. The trip came amid concerns that the coalition might be fraying, worries that intensified after allies including the Saudi defense minister and Jordan’s King Abdullah II made summer visits to Moscow.

“The sense was that even as Russia was planning operations with Iran, [Putin] was trying to peel away U.S. coalition allies,” said a senior administration official, “arguing that the U.S.-led plan wasn’t working.”

The Senate and House intelligence committees have begun examining whether U.S. spy agencies missed signals of Russia’s intentions in Syria despite tracking the buildup over a six-week span.

“I don’t know that we foresaw that [Putin] was going to come rushing in with troops and aircraft,” said Rep. Adam B. Schiff (D-Calif.), a member of the House Intelligence Committee. “But I don’t know, frankly, that Putin knew that he was going to do that until he made the decision. . . . I’m not sure even Putin’s inner circle would have seen it coming.”

U.S. spy agencies now face questions about the potential scope and duration of the Russian campaign, as well as its impact on the CIA program launched two years ago to support moderate rebel groups caught between Assad’s army and extremist elements including the Islamic State.

An initial round of talks between defense officials in Moscow and Washington to set rules to “deconflict” air operations between the two countries, held Oct. 1, brought little result. Late Friday, Pentagon press secretary Peter Cook said a second round of such talks would take place “as soon as this weekend.”

Although Russia’s intervention has been interpreted as a move to prop up Assad, several U.S. officials said Putin’s priority is protecting Moscow’s interests and influence in the region — including a long-standing military base in Syria — rather than ensuring that Assad stays in power.

One U.S. official said Russia could still turn against Assad, picking a replacement from within the regime and bolstering Putin’s ability when the conflict ends to “negotiate a settlement favorable to Russia.”

The decision to dismantle the Pentagon’s training program — whose small teams of fighters were often quickly captured or surrendered their weapons to rival rebel groups in Syria — may force Obama to weigh ramping up support to the CIA-backed groups.

U.S. officials said those involved in the agency program are already exploring options that include sending in rocket systems and other weapons that could enable rebels to strike Russian bases without sending in surface-to-air missiles that terrorist groups could use to target civilian aircraft.

“We could give them better technical systems that are more accurate or can fly a little farther, and intelligence to support that kind of targeting,” said White, of the Washington Institute. “But frankly I think it goes against the grain of what Obama wants or is willing to do in Syria.”

Ellen Nakashima and Craig Whitlock contributed to this report.