Four French former hostages arrived back in France on Wednesday after three years in the Sahel desert held by al-Qaida militants, but questions persisted over whether France had paid a controversial ransom of over 20m euros for their release.

The four were part of an original group of seven people taken from their beds in September 2010 at a well-guarded compound in the northern town of Arlit in Niger where the French state-controlled nuclear giant Areva operates a uranium mine. After over 1,000 days in captivity in harsh conditions, having been separated and moved from hideout to hideout, the four men were retrieved in northern Mali on Tuesday.

French foreign minister Laurent Fabius, who accompanied them back to Paris, said the men were in shock on their first night of freedom in the Niger capital, having been isolated for so long. "They slept well, but on the floor as they are not yet able to sleep on mattresses," he said.

Theirry Dol, 32, a plant engineer, originally from Martinique, described his captivity as "the ordeal of a lifetime".

The story of the kidnapping shook the French government in 2010, furious that such a strategic complex protected by armed guards could have been so easily breached by al-Qaida militants in pick-up trucks, who arrived just after 3am on 16 September, bursting into homes on the complex and pulling out their targets.

Daniel Larribe, 62, a mining engineer who worked as a director of uranium production, had only been back at the site for three days with his wife Francoise after a stint in Namibia, when militants kicked in the couple's door on the compound.

Francoise would later tell Le Monde: "They burst in with Kalashnikovs. Daniel went out straight away, then they came for me in the bedroom and I was taken as I was: barefoot and in pyjamas. Daniel was already lying in the pick-up when I was made to get in. I've never seen his face like that, he never thought they'd take me too."

Around 160 days later, in 2011, Francoise, who was ill, was released along with two African subcontractors who had been taken, a Togolese worker and one from Madagascar, who was suffering from diabetes. At the time, French media reported that a large ransom had been paid for the three, possibly by the companies Areva and Vinci responsible for the plant. Authorities denied a ransom was paid.

Daniel Larribe was separated from the rest of the group and kept with no radio or access to the outside world, unaware that his mother in France had died during that time. Arriving back at an air force base north of Paris, his daughters said Larribe, gaunt and with a long beard, was "well, hadn't lost his sense of humour" and had described a failed escape attempt. They said of their mother's earlier return, distraught and without her husband: "Our mother never really came back, now it feels like we've got both our parents back."

Other French hostages released included Marc Feret, 46, a former marine who, at the time of the kidnapping, had been just about go home to Madagascar where his wife was to give birth to their second child. He met the three-year-old boy for the first time upon landing in Paris.

The youngest hostage, Pierre Legrand, 28, had been on a 15-month volunteer in business scheme and was just about to embark on his journey home to France when he was taken at Arlit.

Both Le Monde and AFP cited sources close to the negotiations that a ransom of over 20m euros had been paid for the four men's release after months of negotiations. The French government repeatedly insisted that no ransom was paid, and no assault took place. Areva also said no ransom had been paid.

After his election in 2012, the Socialist French president François Hollande signalled a U-turn in French strategy, announcing an end to any practice of paying ransoms for hostages. But suspicions had persisted that Paris continued to pay out, causing tensions with partners such as the US.

Reuters reported that the Nigerian Islamist sect Boko Haram was paid an equivalent of $3.15m by French and Cameroonian negotiators before freeing seven French hostages in April, citing a confidential Nigerian government report.

Western and regional security officials have said kidnapping has earned al-Qaida in the Islamic Maghreb, or AQIM, tens of millions of dollars in recent years – a lucrative funding activity, although no figures have been confirmed. In January this year, when thousands of French troops intervened in northern Mali to contain Islamist groups which had gained control of the desert north [http://www.theguardian.com/world/2013/jan/13/mali-high-stakes-francois-hollande], there had been fears that the hostages, thought to be in that region, would not survive. French forces failed to find them in northern Mali, including reportedly narrowly missing them in Timbuktou.

Hollande, meeting the freed hostages at the Paris airbase, warned that there were still seven French citizens being held hostage, three in Africa and four journalists in Syria, talking of an "unbearable wait" for those families.

The freed Niger hostages declined to speak to the media.