An American family have revealed the extraordinary email which has convinced them that their pilot father is alive years after vanishing in Africa without trace.

US pilot Jerry Krause was at the controls of a routine flight from South Africa to the West African country of Mali where he was working as a missionary on April 7, 2013 when he simply disappeared.

The last message from his Beechcraft 17 1900C 17-seat passenger plane was to a control tower on the tiny island of São Tomé, saying he was nine miles from its shore. Then he vanished.

But now his family have received an email from one of his friends - who they believe is a former U.S. intelligence officer with high-level contacts in the government - saying that he is definitely still alive.

They told DailyMail.com that now they fear he is being held hostage by a criminal gang and used to smuggle weapons and drugs around Africa against his will.

The astonishing claim turns what had seemed like a routine tragedy into a mystery which spans two continents, five countries and involves claims of a U.S. government cover-up.

Missing: American missionary and pilot Jerry Krause (pictured with his wife Gina) disappeared during a routine flight from South Africa to the to Mali where he was working on April 7, 2013

The last message Jerry ever sent from his his Beechcraft 17 1900C 17-seat passenger plane before vanishing was to a control tower on the tiny island of São Tomé, saying he was nine miles from its shore. The small aircraft had no black box and he did not send out a mayday call

Krause was working as a pilot for an aviation company in Mali when his job took him to South Africa where he was to pick up an aircraft and fly it back to Mali for refurbishment.

After he vanished his family organized a search in the area around San Tome, São Tomé and Príncipe, an island country about 350 miles off the coast of the African country of Gabon, but were left with nothing: there was no debris, no May Day call, and no black box. His emergency transponder had never been triggered.

They also commissioned air crash investigator Phil Schlener to retrace every step that Krause had taken searching for clues.

According to Schlener he is 99 per cent sure Krause's aircraft crashed into the Gulf of Guinea due to 'heavy thunderstorms' and that the plane plummeted into the ocean some 20 miles off the shoreline.

But he said he had to maintain a one per cent possibility that Krause was hijacked due to his 'cell phone apparently ringing in Angola', absolutely no trace of his or his aircraft whereabouts, and the fact that he seems to have flown this flight in an uncharacteristically 'not by the book' manner.'

That seemed so improbable as to be impossible; the devastated Krause family was accepted that their husband and father was gone and they began to mourn his death and rebuild their lives.

But that was not to be the end of the matter.

DailyMail.com has learned that the family was approached by a U.S. government source in 2014 claiming to have information about Krause's disappearance.

Krause's family organized a search in the area around San Tome, São Tomé and Príncipe, an island country about 350 miles off the coast of the African country of Gabon, offering a $5,000 reward

Jerry was on a routine flight from South Africa to Mali and last heard from near Sao Tome. After his disappearance there were claims he was seen in Namibia and that his cell phone rang in Angola

The source, who the family are calling Sydney, was a former government operative who worked in the intelligence community in West Africa at the time Jerry vanished and a friend of his before he vanished.

The family know her identity, but are choosing not to name her. The following year Sydney said Krause was alive - but the shocking information was scant and there was little the family could do.

Then in 2016 - three years after the disappearance - the case took another bizarre twist.

The family was contacted by someone else who had taken an interest in Krause's disappearance.

They said they were aware of an accident report compiled by the South African government and had emailed the South African Civil Aviation (SACAA) asking why the report wasn't online.

A reply from Albert Phuti Morudi, a senior official at the SACAA and who had cc'd three other people working at the authority, said: 'The accident in question is in a process of being re-opened as a result if (sic) new evidence which was provided to us, it is for that reason it was removed from our website.'

The official said he would re-post the report after they get approval from 'our minister' to review it.

The Krause family saw this as a significant development but when they asked the SACAA to see it, the authority denied it existed.

The authority's spokesman, Kabelo Ledwaba, told DailyMail.com that the email was been sent in 'error', with the official confusing Krause 'crash' with a separate crash investigation.

He added: 'The South African Civil Aviation Authority also wishes to take this opportunity to clarify that at no point did its investigation team produce an accident report relating to this particular accident; meaning that our investigators were not part of the investigation and therefore could not produce any accident report.

'Comments that indicate that the SACAA had published an accident report are therefore inaccurate.'

Gina Krause, 58, is said to be 'up and down' with her emotions and the family have launched a Facebook page called Help Find Jerry

Jerry's family remains hopeful that they will see their father again but say 'there's no way he will come back the same person, there's no way,'

The family then turned to respected private investigator Logan Clarke for more assistance.

Clarke reached out to contacts at the Pentagon and in other departments in Washington.

'The message came back that they had found information on Jerry Krause but they weren't authorized to provide the information, they were shut down,' said Clarke.

The family also reached out to a senator and a congressman who informally approached to the State Department - but that also failed.

'They were told they didn't have the right level of security clearance to access the information they were looking for,' Clarke said.

'They did a favor in checking on this and were totally shut down. This isn't a straightforward disappearance, something else is going on here.'

But the intrigue was reopened, not ended, when 'Sydney' emailed the family in September to say that her associate had traveled to Ondangwa, Namibia where the pilot was last seen.

The email states: 'It was during this time that it was learned that while Jerry was dealing with mechanical issues that someone could have easily gained access to the airplane, hidden themselves and taken over the plane while the storm was oncoming to make it look as if Jerry had crashed.'**

Private investigator Logan Clarke reached out to contacts at the Pentagon and in other departments in Washington and was told they weren't authorized to provide the information

The source said their investigation found a lot of activity from Krause's cell phone in Northern Angola.

They tracked the activity to Ambriz airport, which is a private airport with minimal security in the Bengo providence of Angola.

'Sydney' wrote: 'It was there, where we came in contact with a source that was linked to an organization that had been targeting the west coast of Africa.

'It is with is (sic) information we had learned that a plane and a pilot matching Jerry's description had been seen at Ambriz. It is here where we knew Jerry was still alive.'

Sydney said the belief is that the organization had taken Krause to 'transport items and people back and forth', adding: 'We knew he was still being forced to fly.'

She added: 'As I said on the phone with you, I have seen for my own eyes that Jerry is still alive. As more information is released I will keep you informed.'

A close friend of Krause, Jim Vanderburg, believes he is still alive and was kidnapped. He described Jerry as a 'practical' guy and a 'conservative' pilot who did not take risks'

DailyMail.com is unable to verify any of the information offered to the family by Sydney.

Clarke said: 'She says she saw a picture of Jerry taken in the last year and she knows for a fact he is alive.

'She has access to some sort of government file on this but there's only so much she can say.

'I tried going through my government connections but they have been shut down.

'Somebody does not want this out and our only option is to go public, I'm gonna keep poking this bear until it gets really loud.'

A close friend of Krause, Jim Vanderburg, is also convinced he's still alive: 'For the last four years I believed Jerry was dead, I was convinced of it.

'But when I realized there was a cover-up I knew there was more to it and after looking deeper into it I'm convinced he's alive.'

Jim, 61, from California, who is also an experienced pilot who flew with Krause for five years in Africa, said the new information is compelling and he believes the theory that Krause has been kidnapped.

He described his friend as a 'practical' guy and a 'conservative' pilot who did not take risks.

'Jerry was in Africa because of his Christian faith like I was, he wanted to help people, he was one of the missionaries, that was his heart,' he said.

'His disappearance has left a vacuum in everyone's lives. It is a huge blow to all of us.'

Krause's youngest daughter, Jessica, who lives in Indianapolis, said her family had contacted the president and other senior government figures for help, but their pleas have fallen on deaf ears.

The dream of bringing her father back home is still very much alive, however.

'To be honest there were so many things that didn't add up when my dad went missing, all these little details that were red flags,' she explains.

'It all led us to cling to the belief that our father was still very much alive and we haven't lost that hope.'

Krause had worked in Mali with his wife Gina since 1996, first as a pilot for Mission Aviation Fellowship, a religious group that flies aid to people in need, and then as the director of a for-profit aviation company.

Jessica said that he had in fact previously been held captive.

'He's had a gun held to his head before, this is not the first time his life has been in danger,' she said.

'My family was living in the Congo when a war broke out and my dad was part of an evacuation, he ended up landing at an airport when he shouldn't have and he was held hostage there for three days. He was eventually let go.'

Her mother Gina, 58, is 'up and down' with her emotions.

'It's hard, your imagination runs wild,' she explains. 'It's been very tough for my mom, for all of us.'

Jessica and her two siblings, Nathan, 29, and sister Alyssa, 27 are realistic about the difficult times ahead even if their 59-year-old dad is found.

'After four and a half years as a hostage there's no way he will come back the same person, there's no way,' she said.

'My dad was the glue for the family who brought us all together.

'He's super smart and he really cares about people, with us kids he always made sure we tried our hardest and did our best.

'He is a really laid back guy, he doesn't get stressed out easily and he's a tough character, if anyone can handle this my dad can. He thinks on his feet, calculates risk and really is able to work through high stress situations and come out on the other end.

'I suppose the unbelievable part is how he has not been able to escape after all this time.'