The UK government’s policy of deporting some failed asylum seekers on private jets is facing serious questions after it emerged that the Home Office spent £14m on the practice in the 18 months to June. Many of those earmarked for the flights did not board the planes, leaving many flights half empty.

Earlier this year, a Moroccan – convicted cyberterrorist Younes Tsouli – was chartered a private jet alone so he could be deported back to his country. Many other charter flights flew less than half empty.

In September 2014, 29 Afghans were flown home on a 265-seater plane while 26 Albanians were returned on a 202-seater. At the end of August, a charter flight to Afghanistan took off with 11 failed asylum seekers on board. The Home Office confirmed in a freedom of information request that 96 of the 107 people earmarked for the flight did not fly in the end.

The costs of some charter flights to the government are far higher than published figures suggest because of high court challenges to prevent removals. In the case of the August charter flight to Afghanistan, 61 high court injunctions were granted to Afghans due to board the flight cancelling their departure. This is likely to have cost the government tens of thousands of pounds in legal fees on top of the flight costs.

But once the government has booked a charter flight there are significant cost implications if they cancel it. Government lawyers told the high court in the case of the August charter flight to Afghanistan that if it was cancelled they would have had to pay £300,000 to the flight company.

Charter flights are particularly feared by refused asylum seekers. They do not appear on airport boards and usually the flight numbers bear the prefix PV. Some resist removal, fearing torture or death following a forced return to their home country. Jimmy Mubenga feared removal to his home country of Angola and died in October 2010 after being restrained by three G4S guards. On commercial flights such as that boarded by Mubenga other passengers are able to witness any violence but this is not the case on charter flights.

One Afghan asylum seeker, who had his seat on the August charter flight to Afghanistan cancelled following the high court action, told the Guardian: “On a charter flight there are no ordinary people to witness any struggles between asylum seekers and escorts. Nobody can hear you scream.”

The revelations about the charter flights come just days after it was revealed that Home Office contractor Serco hired a Hummer to transport a group of asylum seekers from London to Manchester.

The charter flights are controversial both for reasons of cost and because of the dangerous locations to which some of them forcibly return people such as Afghanistan.

At a time when the government says it is doing everything possible to curb public spending, the disclosures about the cost of using private planes are embarrassing.

Keith Vaz, the chair of the home affairs select committee, said: “These are astonishing figures for a government department that is facing huge cuts.”

Solicitor Toufique Hossain, of Duncan Lewis, who was involved in preventing many of the asylum seekers earmarked for the August charter flight to Afghanistan from flying, called on the home secretary to reconsider her policy of forcing people back to Afghanistan, one of the most dangerous countries in the world.

The Foreign Office website issues warnings to travellers about the dangers of going to Afghanistan and the UN Assistance Mission in Afghanistan has reported casualties in the conflict are at an all-time high.

Hossain said: “The home secretary ought to explain why she chose to spend hundreds of thousands of pounds deporting a handful of Afghans on a charter flight.”

In 2014-15 the total cost of deporting people on chartered and scheduled flights was £29.6m. Recent destinations for charter flights included Afghanistan, Pakistan, Jamaica, Albania and Nigeria.

Research by campaign groups Corporate Watch and No Deportations revealed that charter flight costs have increased eightfold in the past decade. Most flights have two to three escorts accompanying each deported person.

A Home Office spokesman said that deporting Tsouli on a flight by himself was the safest way to remove him. He said: “Decisions on return flights take into account the availability of scheduled aircraft routes, the cost of maintaining individuals’ detention and the circumstances of each case. We always seek to use the most cost-effective method of removal possible.

“Although last-minute legal challenges can delay some removals, this government has legislated to make it harder for people to lodge spurious appeals, and we are going further in our new immigration bill.”

The bill would make it easier to remove people by extending the use of the “deport now, appeal later” measure.