Updated July 19, 2014 9:07 p.m. ET
New U.S. intelligence assessments indicate that Moscow likely provided pro-Russia separatists in eastern Ukraine with sophisticated antiaircraft systems in recent days, matching evidence put forward by Ukraine and bolstering charges that Russia was the source of the weapon that shot down Malaysia Airlines 3786.KU 0.00% Flight 17 this week, killing 298.
U.S. officials say they now suspect that Russia supplied the rebels with multiple SA-11 antiaircraft systems by smuggling them into eastern Ukraine with other military equipment, including tanks.
Further, U.S. officials believe the systems were moved back across the border into Russia following the shoot down of the jetliner, buttressing what Ukraine charges is an attempt by the rebels and their Russian advisers to cover up their involvement in the crash.
"The assumption is they're trying to remove evidence of what they did," said a senior U.S. official briefed on the latest intelligence.
The expanding case against the Ukrainian separatists and the Kremlin comes as U.S. and Western leaders have swapped rounds of phone calls since Friday, calling for greater pressure against Moscow and a renewed effort to secure the chaotic crash site in eastern Ukraine and ensure that human remains receive proper attention. Secretary of State John Kerry phoned his Russian counterpart on the issue Saturday. (Follow the latest updates on the Malaysia Airlines crash in Ukraine.)
The added certainty that the SA-11 systems likely were in rebel hands also poses questions about why Ukraine or U.S. officials didn't move more quickly to advise commercial jetliners of potential dangers, if there was time after they learned of possible rebel control of the systems.
Moscow has continued to deny supplying armed separatists with heavy weapons, despite mounting evidence to the contrary put forward by U.S. officials. "We know there are Russian troops inside Ukraine," said a U.S. official. "Russian troops, Russian equipment."
Intelligence disclosures by Ukrainian and U.S. security officials reveal a higher degree of military cooperation from Moscow to the Ukrainian rebels than was understood before the passenger jet was shot down, as well as intricate and detailed coordination by Russian military officials with the pro-Russian rebels in eastern Ukraine.
Russian President Vladimir Putin has expressed condolences to families for the shoot down, but said that the Ukrainian government is responsible for failing to keep the peace in its eastern provinces. The Kremlin has stopped short of blaming Ukraine's military for the catastrophe.
No expert air crash investigators have yet had access to the rural crash site since Flight 17 was shot down on Thursday afternoon, and in the absence of an independent investigation U.S. and regional intelligence officials have been poring over satellite and electronic intercepts seeking clues about the cause of the crash.
Consensus among intelligence agencies is growing that the Buk-M1 antiaircraft systems, also known as the SA-11 Gadfly under the North Atlantic Treaty Organization designation, was the weapon used to down the plane as it traveled from Amsterdam to Kuala Lumpur on Thursday.
U.S. and Ukrainian intelligence officials say that Russia introduced this type of missile battery into the conflict zone in eastern Ukraine earlier this month, significantly altering the threat assessment of the rebels against Ukraine's own military and to commercial air traffic as well.
Ukraine, which has been battling the separatists since the spring, has lost several military planes and helicopters from missiles operated by the pro-Russia militias. The range of these weapons systems, however, was limited and not able to threaten commercial airlines at their cruising altitudes.
Reports that rebels had possession of a Buk-M1 came as early as June 29, when separatists overran a Ukrainian armed-forces base in the conflict zone in eastern Ukraine. The rebels boasted of seizing control of the weapons system in a Russian news report.
The counterintelligence chief at Ukraine's national security service, Vitaly Nayda, said the reports didn't overly worry his government, as Ukrainian armed forces had rendered that equipment inoperative in March, around the time when the fighting in the area kicked off. The missile system remains on the base, but all the warheads had been removed, Mr. Nayda said.
The U.S. picked up the first intelligence more than a month ago about Russia providing increasingly advanced weapons, including air defense systems, to the separatists.
Earlier this month, U.S. intelligence agencies concluded that Moscow had supplied pro-Russian separatists with two older SA-11s, which the U.S. believes were moved across the border from Russia along with the tanks and other equipment.
But the U.S., which detected the shipments, didn't think that the two SA-11 systems were operational.
After the shoot down on July 14 of a Ukrainian cargo plane at an altitude of over 20,000 feet, the U.S. assessment began to change, and the U.S. concluded that either Moscow sent the separatists a new and operational SA-11 or repaired one of the two inoperable units which the separatists already possessed, a senior U.S. official said.
The U.S. believes all of the SA-11s in the hands of the separatists were supplied by Moscow.
Mr. Nayda said that his agency became aware that the rebels possessed three Buk-M1 antiaircraft systems, as of July 14. On that day, a Ukrainian military Antonov An-26 transport plane was shot by a surface-to-air missile, killing two crew members.
Mr. Nayda said that Ukrainian intelligence showed that a three-man Russian military team entered Ukraine along with one of the Buk missile systems. He didn't say when the equipment crossed the border into Ukraine.
U.S. officials privately say they have suspected Russian involvement runs deeper than just delivering equipment to the rebels. Rear Adm. John Kirby, the Pentagon press secretary, said Friday that the SA-11 is "a sophisticated system" and that "it strains credulity to think that it could be used by separatists without at least some measure of Russian support and technical assistance."
Ukrainian security officials said that after separatists who were first at the scene of Flight 17's crash site realized they had downed a civilian airline, Russian military personnel and rebel commanders jointly moved to erase evidence of the Buk missile batteries in the conflict zone.
Photographs and electronic intercepts, compiled by Ukrainian intelligence operatives, show that three Buk-M1 systems were shipped out of eastern Ukraine on flatbed trucks in two waves in the early morning of July 18, just hours after the passenger jet was shot down, according to Mr. Nayda.
He said that a system missing a missile crossed the border in a flatbed truck to Russia at 2 a.m. on July 18, and two other missile systems with a complete set of missiles in their battery crossed at 4 a.m.
Russia has denied it exercises any command or control over the rebels.
The body of U.S. and Ukrainian evidence about the escalating threat in eastern Ukraine early last week poses questions as to why Ukrainian authorities did not halt commercial flights over the conflict zone, given the range of the missile systems suspected in the hands of the rebels.
Ukraine imposed a partial flight ban in the region on flights below 26,000 feet on July 1, after news reports that rebels had gained control of a first Buk system. The government then raised the ceiling of the exclusion area to 32,000 feet on July 14, after the military lost its cargo plane. The Malaysia Airlines plane was flying at 33,000 feet.
Mr. Nayda said the Ukrainian security service lacks hard evidence that the AN-26 was shot down by a Buk system, though he said it was clear that a surface-to-air missile of some sort was responsible. More ubiquitous shoulder-fired, heat-seeking ground-to-air missiles that are viewed as a more common threat to aircraft wouldn't have been capable of reaching the altitude at which the military plane was flying. The incident is being investigated.
Another Ukrainian official with oversight over civil aviation matters said that the government never considered closing off the entire airspace of the eastern region because they never dreamed that the Russians or separatists would target civilian air traffic.
Malaysian Transport Minister Liow Tiong Lai on Saturday rejected accusations that the country's national airline was reckless in allowing Flight 17 to fly over the conflict zone.
"MH17's flight path was a busy major airway," he said. "It flew at an altitude set, and deemed safe, by the local air traffic control. And it never strayed into restricted airspace."
The skies over eastern Ukraine ordinarily serve as a major artery of global air travel, linking flights between Western Europe and Asia and Northern Europe and the Middle East. More than 400 flights generally traverse the area every day, European airspace officials have said.
The shoot-down of Flight 17 could have major consequences for how the global aviation industry operates around conflict zones. "This has changed everything," said Tim Clark, president of Emirates Airline, the world's biggest carrier by international traffic. "We will no longer rest on the protocols we had in place that we honestly thought were safe."
Ukrainian officials now have entirely closed off airspace in the region.