The remains of at least 200 people and the black boxes from the downed Malaysia Airlines plane arrived at this eastern Ukrainian city Tuesday in preparation to be flown to the Netherlands, amid confusion over exactly how many bodies have been recovered and evacuated from the crash site.

Jan Tuinder, head of the international team of forensics experts waiting in Kharkiv to fly the bodies to the Netherlands for identification, said the team had removed 50 bodies from the train that brought them from the town of Torez in rebel-held territory, a journey that took more than 17 hours.

The team will methodically open the remaining refrigerator cars containing the body bags in the coming days, taking them out one at a time to ready them for an international flight. The bodies are being prepared for transport in an empty warehouse at a sprawling compound that is a munitions factory where tanks were built in the Soviet era.

The total of 200 bodies that Tuinder said he was informed were aboard the train was far fewer than the 282 bodies that Ukrainian officials said had been recovered from the crash site. The discrepancy appears to reflect uncertainty and confusion at the crash scene, where many of the bodies were picked up and taken to the train by rebels who control the area.

Tuinder’s team is not opening the body bags for a count but instead is placing them in coffins that will be flown to the Netherlands beginning Wednesday morning. It may take several days to complete the task, said Ukrainian Deputy Prime Minister Volodymyr Groysman.

Groysman made a point of saying the black boxes retrieved from the wreckage are in the possession of the Malaysian government, supervised by specialists from the Netherlands and the International Civil Aviation Organization. They were “not for a single moment” under Ukrainian control, he said. The rebels were adamant that they would not turn over the flight data recorders to their enemy, the Ukrainian government.

In Washington, officials said they have evidence backing up their contention that the passenger airliner with 298 people aboard was shot down by an SA-11 missile fired from separatist territory. U.S. officials had said that they had “indications” of sophisticated anti­aircraft systems being moved from Russia into eastern Ukraine and being trucked out of rebel-held territory after the downing of the Malaysia flight.

The delivery of the bodies and the plane’s data and cockpit voice recorders offered some hope that an international investigation might clarify how the civilian airliner was shot down. But experts warned that the crash site has been compromised.

In a nearby village, pieces of the plane that appeared to have shrapnel marks and could be important for any investigation into the causes of the crash sat untended at the side of the road.

The vast main site of the plane crash was secured by two men with rifles Tuesday, despite an international outcry for an impartial investigation to begin there as soon as possible.

Small pieces of plane debris blew in the wind as grasshoppers buzzed in the wheat fields. No one was inspecting the fields except journalists, and there were no other guards across the broad fields beyond the two men who idled on chairs 200 feet from a large piece of the fuselage.

One makeshift memorial had sprung up on the side of the road, underneath an Orthodox cross, dedicated by the village where bodies were collected on the refrigerated train cars that were delivered to Kharkiv.

Satellite image of the debris field near Hrabove

“To the victims of the plane catastrophe from the people of Torez, with condolences,” read an inscription on a wreath, alongside a pile of roses.

The train arrived in Kharkiv shortly after noon, met by about 90 forensics experts and 30 diplomats, according to Groysman. They bowed their heads for a moment of silence.

“It was a very emotional moment when the train stopped,” ­Tuinder said. “It was a very respectful moment. It was very quiet.”

The bodies were taken to the Balashovka Railway Station, a small secondary station with Greek columns, a green tile roof and gardens of flowers that filled the air with a sweet aroma. The locomotive was switched, and the cars containing the bodies were taken across the street to a building at an empty warehouse in the large compound that makes up the Malysheva factory.

The remains were being processed by forensics experts from the Netherlands, France, Malaysia and Australia — all countries whose citizens died in the crash. The process of identifying the remains will be done entirely in the Netherlands.

The final tally of bodies that have been collected and delivered should become clearer in coming days when the body bags are opened and tested for DNA.

Tuinder said confusion at the crash site may have resulted in a miscount, with body parts from one person bundled with body parts belonging to another person.

“What I am sure of, absolutely sure of, is that the bodies in the train, at this moment, in this city, are the remains of 200 persons,” he said, allowing that the final tally could be higher.

Tuinder said he obtained the figure of 200 bodies from the Organization for Security and Cooperation in Europe. An OSCE spokesman in Donetsk cited a higher count.

“The last number we were told was 290,” Michael Bociurkiw of the OSCE told reporters in Donetsk on Tuesday when asked about the discrepancy. “We had no possible way to verify that count.”

When the team visited the site Tuesday, “fighting could be heard in the distance,” he said. “That obviously remains a concern.”

Dutch Prime Minister Mark Rutte said the Netherlands would observe its first national day of mourning in more than 50 years on Wednesday, when planes carrying the first remains of victims are scheduled to arrive at an airport in Eindhoven. The Dutch king and queen are expected to attend an arrival ceremony, along with Rutte, other government officials and foreign dignitaries.

British Prime Minister David Cameron tweeted Tuesday that British air accident investigators would analyze data from the Flight 17 black boxes, in response to a Dutch request.

In Kuala Lumpur, Malaysian Prime Minister Najib Razak said Tuesday that separatist leader Alexander Borodai had lived up to two of the three agreements he had made during behind-the-scenes negotiations that resulted in the handover of the black boxes and the remains. He said the rebels have not yet granted “full access to the crash site so that the investigation may begin.”

Birnbaum reported from Donetsk. Anthony Faiola in Berlin, Annie Gowen in Kuala Lumpur, Natasha Abbakumova and Karoun Demirjian in Moscow, William Branigin in Washington and Ferry Biedermann in Amsterdam contributed to this report.