The rare, high-level talks come a day after US officials said a Russian jet made contact with a US MQ-9 Reaper drone, forcing it to be shot down. Moscow has denied that a collision occurred.
The incident would mark the first time that US and Russian military assets have made contact since the war in Ukraine began in February of last year, and it has fuelled concerns of a potential escalation between the two countries.
But Austin appeared to show restraint during a news conference at the Pentagon, saying the US takes “any potential for escalation very seriously and that’s why I believe it’s important to keep the lines of communication open”.
“As I’ve said repeatedly, it’s important that great powers be models of transparency and communication, and the United States will continue to fly and to operate wherever international law allows,” Austin said.
“It is incumbent upon Russia to operate its military aircraft in a safe and professional manner.”
Contact between the top US and Russian defence officials has been relatively rare since Russia launched its full-scale invasion of Ukraine on February 24, 2022.
Austin and Shoigu first spoke about Russia’s offensive in May of last year, and in October, they spoke twice in three days amid a heightened threat of an escalation in the conflict.
On Wednesday, Austin reiterated the US version of what happened over the Black Sea this week, saying a Russian fighter jet intercepted the US drone in international airspace.
“This hazardous episode is part of a pattern of aggressive, risky and unsafe actions by Russian pilots in international airspace,” Austin said during the news conference alongside US Joint Chiefs of Staff Chairman Mark Milley.
The US officials also said the Russian jet dumped fuel on the $30m drone before the collision.
Milley said there were still questions as to whether Russia meant to down the drone, even though the moments that led up to the crash were “intentional”.
“We know that the intercept was intentional. We know that the aggressive behaviour was intentional,” he told reporters.
“You’ve heard about the dumping of fuel and everything else. We have video evidence of all that so there’s no question that that part of it’s intentional,” he said. “The actual physical contact of the aircraft – that, I’m not so sure. So we’ll have to figure that out.”
Milley added that recovery has been hampered by the fact the drone went down in 1,219 to 1,524 metres (4,000 to 5,000 feet) of water, but said the US had already taken measures to guard against a loss of sensitive intelligence if the drone were to be recovered by Russia.
“We’re quite confident that whatever was of value is no longer of value,” he said.
Milley added that he planned to talk to his Russian counterpart, Valery Gerasimov, the chief of the General Staff of the Russian armed forces, about the incident.
Russia has maintained that while its fighter jets intercepted the drone, no contact was made and instead the US aircraft went down during a “sharp manoeuver”.
It also has said that the drone entered an area that was declared off limits by Russian authorities. Russia has declared broad areas near Crimea off limits to flights.
Speaking after being summoned by the US Department of State over the incident, the Russian ambassador to the US, Anatoly Antonov, said he told US officials that Russia would “no longer allow anybody to violate our waters”, the TASS news agency reported.
Antonov said the drone “deliberately and provocatively was moving towards Russian territory with transponders turned off”.
He said his meeting at the State Department was constructive and the issue of possible consequences for Moscow over the incident was not raised, the RIA state news agency also reported on Wednesday.