At least 10 detonators working for the Halo Trust in the northern province of Baghlan in Afghanistan have been killed and more than a dozen injured.
Afghan officials blamed the Taliban, saying that the militants had “just started shooting everyone”.
But Halo Trust CEO James Cowan told the BBC that “the local Taliban … came to our aid and intimidated the attackers.” The Taliban also denied the attack.
Violence worsened as the United States began withdrawing its last troops on May 1.
The departure of international troops comes at the center of a closing period in the peace talks between the Afghan government and the Taliban.
Several areas in the province of Baghlan have witnessed fierce fighting between the Taliban and government forces.
Workers were killed when gunmen stormed the complex at 21:50 (17:20 GMT) on Tuesday after spending a day clearing mines from a nearby field.
Interior Ministry spokesman Tareq Arian told reporters that “the Taliban entered a mine clearance agency center … and started shooting everyone.”
But the Taliban issued a swift denial.
“We condemn the attacks on the defenseless and regard them as cruelty,” the militant group spokesman Zabihullah Mujahid tweeted. “We have normal relations with NGOs. Our mujahideen will never carry out such cruel attacks.”
Mr Cowan of the Halo Trust told BBC Radio 4 Today that the attackers went “to bed” shooting workers “in cold blood”, but that the local Taliban helped the deminers.
“I think it is important to know that the Taliban have denied responsibility for this, and indeed the local Taliban group came to our aid and scared the attackers,” he said.
“We don’t know who the attackers were – we might guess on that, but I won’t – but I think we have the capacity as Halo Trust to act on both sides of the line in this terrible conflict,” he added.
In a police clip from Baghlan shared with reporters, the survivor of the attack said gunmen asked if any of them belonged to Hazara’s minority community before opening fire.
“Five to six armed men came and took us to a room,” he said. “First they took all our money and mobile phones, and then they asked who our boss was. They asked, ‘Is there any Hazara here among you?’ We told them, ‘We don’t have Hazara here.’ ”
He added that he was shot in the head, but managed to escape through a window.
The Hazaras, the third largest ethnic group in Afghanistan, have suffered long-term discrimination and persecution, largely because of their Shiite faith. In recent years they have suffered kidnappings and killings at the hands of the Islamic State group and the Taliban.
The Halo Trust was established in the UK in 1988 to dispose of remaining bombs from the Soviet occupation of Afghanistan for almost a decade.
He was supported by Princess Diana and her son, Prince Harry.