More than 3,000 refugees and militants have crossed the Lebanese border into Syria in the second phase of a repatriation that aid groups say lacks transparency and offers few guarantees about the returnees’ welfare.

The returnees, among them up to 350 militants who had lived near the Lebanese border town of Arsal, were escorted on Monday by Hezbollah, the powerful armed group based in Lebanon, to nearby towns in Syria’s Qalamoun region. It followed a transfer earlier this month of more than 7,000 refugees, fighters and their families to Idlib province in northern Syria, which is largely controlled by al-Qaida-inspired groups.

The UN played no role in either repatriation and has cautioned that the conditions for safe return have not been met. Although they have been cast as voluntary, some senior UN officials believe many of those who have crossed into Syria have had little choice in their departure and that the move has been contrived to suit political ends.

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Arsal had been a focal point of clashes between the al-Qaida-inspired Hayat Tahrir al-Sham – formerly known as Jabhat Fateh al-Sham and Jabhat al-Nusra – and Hezbollah over the past 18 months, and Lebanese leaders had frequently claimed that extremists based there amid an estimated 100,000 refugees had created a lawless enclave to terrorise locals and menace Lebanon.

But more recently, the fate of the besieged town had become central to a broader debate over how to deal with the millions of Syrians displaced into Lebanon, Jordan and Turkey by Syria’s seven-year war.

The removal has come against a backdrop of increasingly strident rhetoric against refugees in Lebanon, with some of the discourse driven by politicians whose fates are tied to the fortunes of the Syrian leader, Bashar al-Assad.

More than 1 million Syrians are registered with the United Nations high commissioner for refugees (UNHCR) in the Lebanese capital, but at least another 500,000 are thought to be scattered throughout the country. An extensive aid programme has largely covered the cost of the influx.

Syrians in Beirut have increasingly claimed that the government is attempting to push them back to Syria, where the Assad regime has gradually clawed back control over many parts of the country, with extensive backing from Iran and Russia.

Despite a slowdown in the fighting, much of Syria remains ravaged by war and refugees have expressed fears that they would be vulnerable to persecution if they returned. “The pressure to leave is mounting,” said Nabil al-Homsi, a long-term refugee in Lebanon. “They want us to pretend that everything is OK [in Syria], that we are more vulnerable here than we would be there. The Lebanese don’t want us. It’s an uncomfortable time.”

Aid groups say there is increasing concern that extensive refugee populations in Lebanon and Turkey are also being pressured to consider returning to Syria. NGOs working on Syria issues in Turkey say they have found it increasingly difficult to renew work permits or to conduct cross-border work. “There is a clear push to make us go away,” said one senior official. “The refugee issue is politically more difficult for [the Turkish government] than it has been. And they are passing that down to us.”

While Ankara has not struck a rapprochement with Assad, the government of Turkey’s president, Recep Tayyip Erdoğan, has told Russia and other allies that the survival of the Syrian leader has become a political reality. A strident opponent of the Assad regime for the first five years of the war, Turkey has since framed its interests through the prism of stymying Kurdish ambitions, and countering the threat from Islamic State. It still supports a refugee population of more than 2 million, but its borders with Syria have been closed to civilians fleeing the conflict for much of the past two years.

Facebook Twitter Pinterest Vehicles make their way through Lebanon as part of the repatriation. Photograph: Anadolu Agency/Getty Images

Bassam Khawaja, a Lebanon researcher for Human Rights Watch, said: “We’re very concerned about the lack of safeguards or any process in place to ensure that these returns are completely voluntary. Any forced or coerced returns would be a violation of Lebanon’s obligations under international law.”

The returnees who departed on Monday arrived late in the day at three towns close to Damascus, where they have received offers of amnesty. Some of those who left said they feared they would be sent further, to Idlib, where refugees who departed Arsal a fortnight ago are still settling in.

“I worked as a doctor in Arsal at the Central hospital and at the Islamic hospital,” said Dr Hassan Ammar, 24. “It was a mistake coming here to Idlib, there is no work. I lost everything and the ride in the bus was from hell. Jabhat al-Nusra was the main opposition group operating in Arsal, we were almost separated, it was like the civilians alone and the militants alone. They didn’t really protect us from the menace of the Lebanese army and Hezbollah. They had their own backs to watch after.

“So I am here in Idlib now, miserable, but at least we have fresh vegetables and can roam around without feeling targeted. Hezbollah is stronger than both the Syrian and the Lebanese army. I was there for about five years, it felt like everything was under their control, no one else’s.”

A second new arrival, Diab Hussain al-Zaitoun, 27, said: “I had to leave Arsal, conditions were horrific. What can I tell you? I am at a loss for words … I feel relatively safer here although we don’t know if we might be bombed into pieces at any given time – it’s an unknown type of safety. I don’t have a job here. But anything beats being in Arsal surrounded by the thugs.”