WASHINGTON >> A barrage of missiles in Syria by U.S., French and British forces most likely will not stop President Bashar Assad’s chemical weapons program, a Pentagon assessment has concluded, despite President Donald Trump’s “Mission Accomplished!” declaration hours after last weekend’s strikes.

The military intelligence report, put out less than three days after the attack, said the allied airstrikes likely set back Assad’s production of sarin gas.

But it found that the Syrian president is expected to continue researching and developing chemical weapons for potential future use, according to a U.S. intelligence analyst who has seen the document and described it to The New York Times on the condition of anonymity.

“They do retain a residual capability” to produce chemical weapons, Lt. Gen. Kenneth F. McKenzie Jr., the Joint Staff director, said Thursday of the Syrian government. He said the chemical weapons are “spread through the country.”

“They still have ability to conduct attacks; I would not rule that out,” McKenzie said.

Planning for the strike of 105 missiles on three targets — chemical weapons storage and research facilities near Damascus and Homs — took nearly a full week. Staging and final preparations for the attack, which lasted roughly two minutes, took hours to carry out. Trump announced it Friday night in Washington as the missiles were hitting Syria before dawn Saturday.

Hours later, Trump said on Twitter that the strikes “could not have had a better result.”

Nikki R. Haley, the U.S. ambassador to the United Nations, also told the Security Council on Saturday that the United States is “confident that we have crippled Syria’s chemical weapons program.”

Other Trump administration officials were more circumspect. A senior administration official told reporters Saturday that the Syrian government still possesses sarin, chlorine and weapons able to carry chemicals that could be used for future attacks. Still, the official said, the strikes successfully helped “re-establish the deterrent” by proving that Trump was willing to take military action.

In the end, last weekend’s operation was a textbook example of how the military can carry out a precision strike, seemingly without incident, despite potential complications. It is unclear if all missiles hit their intended targets. Russian state news media said Thursday that Syria found two unexploded cruise missiles after the strikes and has handed them over to Russian officials.

Last weekend’s attack was nearly twice as large as a strike last year by two U.S. warships against a Syrian airfield where officials said Assad’s forces had launched warplanes that dropped sarin gas on the rebel-held town of Khan Shaykhun, killing more than 80 people and sickening hundreds more.

U.S., British and French aircraft and ships fired cruise missiles from the Mediterranean, the Red Sea and the Persian Gulf. Dozens of refueling, reconnaissance, escort and jamming aircraft were airborne. Some of them primarily focused on monitoring and scrambling communications to stymie any Russian and Syrian counterattack, whether with surface-to-air missiles or warplanes, according to U.S. military officials.

Senior U.S. officers were not sure how Russia would respond to the airstrikes, despite a frequently used deconfliction hotline between the two countries to coordinate continuing military operations in Syria. On April 12, intelligence officers from every U.S. military regional command held a videoconference regarding the potential Russian blowback once the missiles were launched, military officials said.

As the U.S. military planned the strikes, the White House and the Pentagon weighed several Syrian installations and bases that might be targeted.

When it came time to attack, most of the operation was executed and overseen by the U.S. naval base in Bahrain, where the 5th Fleet is based, and the air command center at Al Udeid Air Base in Qatar. There, dozens of U.S. and allied planners huddled in front of banks of computers, maps and giant video screens to manage the flow of aircraft and missiles participating from the United States, Britain and France.

The number of warplanes involved also created some diplomatic sensitivity with other countries in the Middle East.

One senior U.S. officer involved in the strike planning said Saudi Arabia and Jordan were put in the delicate position of allowing U.S.-led fighters and bombers to use sovereign air space — so long as it was not publicly advertised.

With those countries’ permission, the United States flew B-1 bombers from Qatar along with one electronic warfare jet and refueling aircraft, Pentagon officials said. The bombers likely launched cruise missiles from Jordanian territory. The missiles, carrying 1,000-pound warheads, are capable of hitting narrow targets from hundreds of miles away; officials later said they were not aware of any civilian casualties caused by the missiles.

A variety of cruise missiles were used in the strikes to distance allied ships, aircraft and one U.S. submarine from a potential counterattack. Though some of the fighter jets may have been within range of some of the enemy’s more advanced surface-to-air missiles — upgraded in the past three years by the Russian military — their pilots, if shot down, would have been able to parachute into largely friendly territory or waters heavily patrolled by friendly vessels.

The military intelligence report indicated that the Barzeh research and development center in Damascus was destroyed, according to the analyst. Most of the missiles were aimed at the Barzeh facility, where the Western allies believed the Assad government was rebuilding its chemical weapons program. It has been closely monitored since the Organization for the Prohibition of Chemical Weapons found precursors for nerve agents there in 2014.

The other two sites — the Him Shinshar chemical weapons bunker and storage facility in Homs — were severely damaged. But the analyst said the report cited surveillance assets that watched a 5-ton truck leave one of those sites the day before it was struck, with a tarp-covered load that could have included equipment or chemical weapons.

Military experts voiced skepticism that the airstrikes severely hobbled Assad’s chemical weapons program.

Claims that the attacks set it back years depend in part on what was inside Barzeh at the time of the strikes, said Jeffrey Lewis, an analyst at the Center for Nonproliferation Studies at the Middlebury Institute of International Studies.

“That might be true if Barzeh was filled with difficult-to-replace equipment or if crucial personnel were killed in the strike,” he said. “But what we see is just a building. Are we certain all the important bits were above ground and destroyed in the airstrike?”

In November, the Organization for the Prohibition of Chemical Weapons inspected Barzeh and collected samples for testing. It concluded last month that inspectors “did not observe any activities inconsistent” with Syria’s obligations under the Chemical Weapons Convention.

Defense Secretary Jim Mattis said chlorine gas was among the weapons used in the April 7 suspected attack on Douma, outside Damascus. But he provided little evidence, nor any that the three targets contained chemical agents banned by a 2013 agreement between Russia and the United States to eliminate Syria’s chemical weapons program.

Chlorine, which is commonly used in industrial products, was not outlawed as part of the 2013 agreement. However, it is described by the Organization for the Prohibition of Chemical Weapons as a choking agent, and is prohibited when used as a weapon; Syria is believed to have used it in several chemical attacks since 2013.

The organization’s inspectors have sought to gain access to the site of the attack in Douma to collect evidence of chemical agents but were forced to turn back after coming under gunfire this week. Russian state news media reported that the Russian military found a rebel chemical lab in the same area.

Mattis on Wednesday blamed the Syrian government for the holdup.

© 2018 The New York Times Company