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The expert group, which Ukrainian authorities said numbered 101 people, was the largest to access the wreckage since Flight MH17 crashed in rebel-held territory on July 17. All 298 people aboard were killed.
Roads had for days been too dangerous to use because of heavy fighting, frustrating efforts to recover all the victims' remains and push ahead with an investigation.
"The team has finished its work for today. They found and recovered human remains. They will... be brought back to the Netherlands for identification," Dutch Prime Minister Mark Rutte said in the Netherlands. "The security situation at the site is unstable and unpredictable."
In the latest clashes, separatist forces killed at least 10 Ukrainian paratroopers in an ambush after midnight near Shakhtarsk, one of the closest towns to the wreckage site, the Ukrainian military said.
The rebels said they had pushed back government forces around Shakhtarsk, where fighting has raged for several days. A Ukrainian military official said a further 13 troops were wounded and 11 unaccounted for.
The recovery mission included experts from Australia and the Netherlands, whose countries suffered a big loss of life in the shoot-down, as well as representatives of the Organization for Security and Cooperation in Europe (OSCE).
"Any body part found gives more relief to the relatives of those who died in that accident and will help also to further identify bodies should it be the only part that is left of a person who died in that accident," Alexander Hug, deputy head of the OSCE mission in Ukraine, told a briefing in Donetsk. .
An advance team drove to the site from the nearest big city, Donetsk, on Thursday but stayed only for about an hour and said sides resumed fighting immediately after they left.
Agreement was later reached to extend the limited ceasefire around the route, making it a safe corridor, at talks in Belarus involving Russia, Ukraine, the rebels and the OSCE.
In a phone call with German Chancellor Angela Merkel on Friday, Ukrainian President Petro Poroshenko promised to stick to the ceasefire, a statement on the president's website said.
Kiev has accused the rebels of planting mines in the region near the crash site, suggesting they want to hamper the investigation and hide evidence, but an OSCE official said no evidence had been found to back up the allegations.
Ukrainian officials said this week about 80 bodies had not been recovered from the wreckage of the Boeing 777. The victims included 196 Dutch and 27 Australians, as well as 43 Malaysians.
Rutte said a total of 400 international experts, including police, forensic experts, military police and investigators were now in eastern Ukraine to help with recovery and investigation.
The United States says the separatists probably shot down the plane by mistake with a Russian-made missile. The rebels and Moscow deny the accusation and blame the downing on Kiev's military campaign to quell the uprising.
Kiev accuses Moscow of supplying arms and fighters to the separatist rebellion, an allegation also made in the West, which has stepped up sanctions against Russia over the crisis.
Russia denies it is involved. The Defence Ministry said on its website that satellite imagery Kiev had released in public to back the accusations was "hastily doctored evidence".
The Ukrainian government also made new allegations on Friday that Russian planes had flown over east Ukraine although Moscow has denied such accusations in the past few weeks.
In other violence, city authorities said five civilians had been killed and nine wounded in the past 24 hours in Luhansk, which, with, Donetsk, is the last big rebel stronghold.
Government forces have intensified their offensive in mainly Russian-speaking east Ukraine since the airliner came down.
The separatists have been pushed out of other towns they held in the rebellion, mounted against rule by Kiev's pro-Western leaders and inspired by Russia's annexation of Crimea after a pro-Moscow president was ousted in Kiev in February.
Luhansk, the smaller of the two main rebel strongholds, is now almost completely surrounded by government troops. It has been cut off from food supplies and left with almost no electricity or running water, authorities say.
More than 1,100 people were killed and nearly 3,500 wounded between mid-April and July 26, the United Nations said. (Additionl reporting by Pavel Polityuk in Kiev, Maria Tsvetkova in Donetsk and Anthony Deutsch in Amsterdam, Writing by Gabriela Baczynska, Editing by Timothy Heritage and Mark Heinrich)