The preliminary results of Azerbaijan’s investigation into the deadly crash of a civilian airliner point to the plane being hit by a Russian antiaircraft missile, or shrapnel from it, said people briefed on the probe.

Azerbaijan’s initial findings came quickly after aviation experts said visible damage to the Azerbaijan Airlines flight—carrying 62 passengers and five crew members—was evidence that it was hit by a munition. The crash killed 38 people, and left 29 survivors, some of whom said they heard a loud explosion that preceded the flight’s problems.

Flight 8243 to Grozny in Russia’s Chechnya region from the Azeri capital Baku suddenly diverted course when flying over a part of Russia where the military had been shooting down Ukrainian drones. The plane went down in western Kazakhstan near the Caspian Sea city of Aktau. Of the survivors, many were in critical condition at hospitals.

The people familiar with the probe said Russia diverted the plane from its airspace and had its GPS jammed. They said Azerbaijan was deliberating over a response to the crash.

Neither the country’s civil aviation agency nor the presidential office responded to requests for comment.

Russia’s Federal Air Traffic Agency said the crash happened after the plane had hit a flock of birds. When asked about the investigation’s preliminary indications of Russian involvement, Kremlin spokesman Dmitry Peskov said it was too early to come to conclusions about the cause of the crash.

Any Russian responsibility for the crash would echo the events around the downing of Malaysia Airlines Flight 17 , which was shot down by an air-defense system used by the Russian military from Ukrainian territory held by Moscow-backed rebels in 2014, killing all 298 people on board. Russia didn’t accept responsibility for that incident.

The potential for a flare-up in relations between Moscow and Baku comes at a delicate moment in the Caucasus region, where Russia, Turkey and Iran are vying for influence. Oil-rich Azerbaijan has maintained pragmatic relations with Russia since the Kremlin’s invasion of Ukraine, but it also has grown closer in recent years to Israel, which has sought to undermine Iranian influence.

About an hour and 20 minutes into the flight, the pilots appear to have started to lose control of the aircraft, likely caused by puncture holes in the plane’s vertical stabilizer, aviation experts said. The crew then battled—for at least 75 minutes—to maintain a constant speed and altitude, with the aircraft rising and falling by as much as 8,000 feet many times until ultimately crashing into the ground, according to data and analysis from tracking specialist Flightradar24.

A passenger on the Embraer 190 aircraft told the Russian television network RT that the plane had tried to descend twice but both times pulled back up. On the third attempt, he said, he and other passengers heard an explosion outside the cabin, and pieces of the aircraft’s shell flew off.

“Everyone heard the explosion,” said Subkhonkul Rakhimov , speaking to RT.

Aviation-security firm Osprey Flight Solutions, citing assessments of footage of the crash, the damage to the aircraft, and recent military activity, said that the flight “was likely shot down by a Russian military air-defense system.” The plane’s undulating flight path—and a sudden downward turn at a dangerously steep angle ahead of landing—suggests the pilots were struggling to guide it, experts said.

At the site of the crash, investigators from Kazakhstan and Azerbaijan pored over the remnants of the plane and were examining the contents of the craft’s black box for more details of the flight’s final path across the Caspian Sea, said Kazakh officials.

Azeri state media said representatives from Embraer were on their way to Kazakhstan to examine the crash site. Russia sent Emergency Ministry planes to evacuate the nine Russians who were injured in the accident.

When it set off from Baku on Wednesday morning, the Azerbaijan Airlines plane was flying over a part of Russia’s North Caucasus that has been targeted by Ukrainian drones in recent weeks. Russia’s Defense Ministry said it had shot down 59 Ukrainian drones overnight into Wednesday, most of them in areas bordering Ukraine.

One of them was shot down over Vladikavkaz, west of Grozny, just three hours before the plane crashed on Wednesday, said the regional governor there, Sergei Menyaylo . On Dec. 15, a drone struck a campus of Russia’s National Guard in Grozny and at least two other drones were shot down by air defenses.

Ukrainian drone attacks across large parts of Russia have recently affected commercial flights, including temporarily halting operations at Kazan airport, about 500 miles east of Moscow, before the crash.

Israel’s flag carrier, El Al, said it was suspending flights between Tel Aviv and Moscow “in light of the developments in the airspace of Russia.” Azerbaijan has become a large purchaser of Israeli arms, and the two countries have boosted security cooperation in recent years, particularly with an eye to stopping Iranian influence in the region.

Neither Azerbaijan nor Kazakhstan has come forward with a definitive version of events, but the growing body of evidence pointing to Russian air defenses had already boosted expectations that Russia should come forward with an official acknowledgment.

“Baku’s expectation is not only an apology but also an explanation as to why the pilots’ request to land was denied and why their GPS was jammed over the Caspian Sea—both of which could have saved the plane and its passengers,” said Zaur Shiriyev , a Baku-based nonresident scholar at the Carnegie Russia Eurasia Center, who focuses on the region.

Militaries often disrupt or spoof GPS signals to disguise their own airborne activities or to affect the targeting of enemy drones and jet fighters. GPS spoofing has been deployed across swaths of southwest Russia since the start of the war with Ukraine.

Air-defense missiles, like those that Russia has against Ukrainian drones, typically explode shortly before colliding with an aircraft, distributing shrapnel similar to that of a grenade that then pierces through the metal of an airframe.

If a Russian missile was responsible for the crash, failure by Moscow to take responsibility would cause a rise in tensions between the two former Soviet republics. The two countries have grown increasingly distant as Turkey’s position has grown in the South Caucasus region while the Kremlin has slowly lost sway.

The Karabakh War in 2023 between Azeri forces and Armenian separatists in the Nagorno-Karabakh region saw Baku, aided by Turkey, claim control over the enclave that, although inside Azerbaijan’s borders, had been long ruled by ethnic Armenians. Russian peacekeepers stationed there to prevent violence did little and were later withdrawn.

Write to Thomas Grove at thomas.grove@wsj.com

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