The coffins were made of wood. The two military transport planes were gunmetal gray. The hearses — 40 of them — were black.

This scene stood perfectly still Wednesday as a tiny nation observed one minute of silence, part of a national day of mourning, its first in 50 years. Trains stopped. Courts suspended trials. Conversations halted. And here, at this military base, the only sound was the metal clang of 17 flags, all hung at half-mast, representing the nationalities of the 298 passengers and crew members who died aboard Malaysia Airlines Flight 17.

Then, on cue, members of the Dutch Royal Air Force began to move. They marched in formation, in two lines, disappearing into the bellies of the massive planes and returning, four on each side, again and again to stiffly carry a single coffin toward a different waiting car.

This was the symbolic end to almost a week of diplomatic wrangling and public worry that focused on who is to blame for the July 17 missile strike on a passenger jet. Dutch officials had struggled to reach the crash site in a disputed region in eastern Ukraine. It had not been clear when these bodies would be returning to the Netherlands. The Malaysia Airlines plane had taken off from Amsterdam Airport Schiphol. The death toll included 193 Dutch citizens.

But this was only the first wave of remains headed for the Netherlands. On Wednesday, just 40 bodies made the journey here for identification and a forensic exam by Dutch officials. Several more trips over the coming days would be needed to complete the task, a Dutch government spokesman said.

The first 40 bodies were flown out of Ukraine even as confusion reigned over exactly how many have been recovered and evacuated from the crash site. Authorities said the remains of at least 200 people have been recovered, along with the Malaysian airliner’s black boxes.

The bodies had been held for days on a train of refrigerated rail cars stuck in the eastern Ukrainian town of Torez, where rebels had balked at relinquishing custody. But by midday Tuesday, the train had made its way to Kharkiv.

In Kharkiv, the coffins of the Flight 17 victims were escorted by a Ukrainian military honor guard past dignitaries, experts and investigators. Among those present were men wearing armbands or T-shirts with the insignia of Interpol and the Organization for Security and Cooperation in Europe. There were also forensics experts from several nations who are tasked with preparing the bodies for transport and finding more remains at the crash site.

Ukraine’s deputy prime minister, Volodymyr Groysman, expressed not only sadness but anger and defiance as he vowed that the Ukrainian government would bring to justice those who fired a missile at the commercial airliner.

“In our common grief, we assure you those people guilty of this terrorist act will be punished,” he said.

At the air base in Eindhoven, the Dutch king and queen watched. So did more than 100 family members of victims. The ceremony was broadcast live across the nation. Just outside the military gates and all along the 60-mile route to a military barracks in Hilversum, where the bodies would be held, thousands of people stood to pay their respects and to glimpse the trailing procession of hearses. Police closed two major highways as the hearses made their way.

“Seeing one car is bad enough,” Sabrina Vaessen, 38, said as the hearses drove past her position along the road. “Now you see 40 of them.”

“And there were only 40,” added Miranda Heusschen, 43, of the same town of Valkenswaard. “They still have to get more.”

“And you know there are children in there,” Vaessen said.

The military transport planes came from the Netherlands and Australia. The Dutch C-130 Hercules carried 16 bodies. The Australian C-17 Globemaster held 24. They began their trip in Kharkiv. A few minutes before 4 p.m., the planes appeared distantly in the sky. They landed one after another, before taxiing to the tarmac in front of a giant hangar, where Dutch royalty, Prime Minister Mark Rutte and victims’ families were sitting, surrounded by members of the country’s air force.

It was a display ripe for interpretation — before the planes were unloaded, a bugler played “Last Post,” a song traditionally used when soldiers die in war.

But a Dutch government spokesman downplayed the suggestion that the military’s large role here was intended to draw notice from anti-Ukrainian forces supported by the Russian government or Russian President Vladimir Putin, who has denied that his country shares any blame for the plane disaster.

There is no message from the military, a Dutch government official said.

“It wasn’t a military service,” said Lodewijk Hekking, spokesman for the Dutch Ministry of Security and Justice. “It was a service with military support.”

But the Dutch do appear to be pursuing sanctions against Russia. The European Union on Tuesday imposed limited sanctions against more Russian businessmen, while avoiding hitting entire sectors of the Russian economy.

Outside the military base, dozens of people stood on a bike path in the summer heat, waiting for the hearses. Several people mentioned how small a country of 17 million can feel. Everyone knew someone on that flight or knew someone who did. Ine van der Linden fell into that second group.

As she leaned against a scooter with her husband, she said she was unsure how to feel about the geopolitical intrigue and threat of sanctions. She only knew how she felt about the loss of so many lives. That’s why she was here. And the explanation was simple.

“It’s very sad, isn’t it?” she said.

Morello reported from Kharkiv. Michael Birnbaum in Donetsk, Ukraine, and Ferry Biedermann in Eindhoven contributed to this report.