A senior missile scientist who defected from Burma after leaking secrets about the junta's suspected nuclear programme has revealed how senior generals were personally involved in plans to develop a weapons system.

In his first in-depth newspaper interview since defecting seven months ago, Sai Thein Win, a major in the Burmese army, said he attended four presentations where the nation's nuclear ambitions were revealed. He gives a rare insight into the shambolic, demoralising conditions imposed on scientists, and reflects on the consequences of his flight on the family he has left behind. The interview was conducted just days before Burma holds its first elections for 20 years, which have been condemned as rigged by rights groups and the international community.

Sai Thein Win now lives in a small flat on the outskirts of a large European city. There is no name on the door and the curtains are closed. The location of his home can not be revealed because he fears that Burma's generals will send someone to try to kill him. "I'm not really here," he said. His room is sparsely decorated, with a table, a computer and a large, sharp dagger.

Sai Thein Win's revelations since he left the country have been described by a former International Atomic Energy Agency head as "truly extraordinary information". Burma's army is closed to the outside world and Sai Thein Win is the main source, and in some cases the only source, for a case with major political implications. Can he be trusted?

International observers fear that the junta has tried to obtain nuclear weaponry as part of its strategy to retain power. But evidence from Sai Thein Win suggests that the programme is so mired in incompetence, corruption and delays that it would take years to develop a nuclear programme.

Sai Thein Win – who has been compared to Mordechai Vanunu, who in 1986 exposed Israel's nuclear weapons programme – said he spent three years working in a factory in the hot desert of western Burma. He said the regime installed machinery for their programme but virtually nothing was made, and employees were bored waiting for designs. At night, they sat drinking whisky and watching TV.

"When we were alone, we sometimes talked about how stupid this was," said Sai Thein Win. "We called ourselves Nato – No Action, Talking Only. We wasted our lives. I'm not a politician, I'm proud to be an engineer and an officer. I would be proud to be the first rocket scientist of Burma but I had no chance to apply what I had learned. It made me upset." The

Burmese authorities have denied that they are developing nuclear weaponry and called Sai Thein Win a deserter and criminal. The country's Foreign Ministry said that it lacked the "infrastructure, technology and finance to develop nuclear weapons".

But in Sai Thein Win's evidence he claims senior leaders of the junta were keen to try. As one of 72 young engineers sent to Moscow for further study in 2001, he said they were waved off by a senior general, Maung Aye. Sai Thein Win said a senior general told them Burma needed nuclear weapons for its protection.

He specialised in missile technology but interrupted his doctorate studies in Moscow. He was appointed production manger to make components for the Burma's missile and nuclear weapons programme. He said he was in a trusted position and had access to confidential material.

On two occasions, he says, he attended presentations of the so-called nuclear battalion at another installation at Thabeikkyin, in central Burma. At one of them, Than Shwe – the leader of the junta – arrived in a car and was led to a room filled with other generals. He sat on a sofa and watched a female scientist give a presentation related to their work. Apparently, Than Shwe was impressed, gave a short comment and encouraged them to continue with their work, said Sai Thein Win.

The scientist said he did not doubt that the intention of the so-called nuclear battalion was to construct a reactor, enrich uranium and build a nuclear bomb. He said he saw documents that proved this but did not steal any to prove his claim.

"Everyone asks me, 'Did I get an order from the generals to create a nuclear bomb?' But I never got my hands on those documents. I had the chance to steal them, but I didn't."

He emphasised that his frustration with problems at the factory was a major reason why he started leaking the information. He said when machines broke, they could not fix them themselves but had to call the German manufacturer, who thought they were for civil use and had to be deceived. "If things went well, I would have still been there," he said. "If they did very professional work, I would be proud to be there. I would be proud to be part of that."

Another factor behind his defection was the suicide of his sister while he was in Moscow. She had worked at a school and earned one-seventieth of what he as a privileged army officer could earn. "The regime gives privileges to the officers, but condemns other public workers," he said. "For me, the pay was good enough, but not for my sister. In that way, the regime was partly responsible for her suicide."

In 2009, he saw a television show from the Oslo-based television channel, the Democratic Voice of Burma (DVB), which spoke of rumours of a nuclear weapons programme, and showed a picture of the factory where he worked. He said he went and bought a camera and took pictures at the factory. A security guard saw him but did not say anything.

So he went to the office, uploaded a picture and sent it to a contact. "After sending the pictures, it was like my thoughts kept circling around this, 'I'm in danger, I'm in danger, I'm in danger!'" He continued to collect pictures, get documents and upload them. "I had to rely on strangers. I felt stupid. If the pictures were publicised before I was out of the country, I would be killed."

He sat in his office during work hours and uploaded pictures to Facebook. DVB, which he was now in contact with, asked for more. He replied that he could give them everything, but that he would have to get out quickly afterwards. He had a fake passport and paid a $400 (£246) bribe for a visa. "If they got me on just one thing, they would find everything," he said. "I wrote nothing down, it was too dangerous. Everything was spinning around in my head."

He managed to get a flight to Thailand where he was met by a representative from DVB. His documents were sent to the former head of the International Atomic Energy Agency, Robert Kelly, for analysis. He has described Sai Thein Win as a "source with truly extraordinary information". The defector revealed hundreds of photographs from inside a factory that show machines and constructions, as well as technical documents that suggest attempts to develop nuclear technology, according to experts. The defector's evidence "correlates well with information from other published and unpublished sources", said Mr Kelly's report.

In his analysis, Nuclear Related Activities in Burma, he wrote: "Our assessment of multiple sources is that Burma is really developing nuclear technology, that it has built specialised equipment and facilities, and it has issued orders to a cadre to build a programme." Mr Kelly has also said: "This is not a good programme, it is not successful and it is not professionally managed."

Sai Thein Win said his email and Facebook page were hacked and he was tipped-off that he had been traced in Thailand. After he left the country, his mother and family were visited by the secret police, put under surveillance and had to inform the authorities if they were planning to leave Rangoon, he said. The Burmese authorities have called the accusations about the nuclear programme "unfounded" and said that Burma "only wants peace and has no ambition to become a nuclear-power state".

If Burma's nuclear ambitions are substantiated, it will raise questions about whether the junta – which has run the country since 1962 – is receiving help from rogue nations such as North Korea. Finally, when asked what he wanted to tell those who suspected he had made up his story, Sai Thein Win said: "Go and see for yourself. And wait for more to escape with evidence. I've done my best. I've done everything I could."

Sai Thein Win: Life in brief

Sai Thein Win grew up in the village of Kyaukme in Shan state in north-eastern Burma with mountains on all sides. His father was a clerk; his mother stayed at home. He went swimming, boxing and played the guitar – but one interest had his special attention: weapons.

He created traps, caught birds and studied guns and missiles. At 18, he applied for the military. Because of his good grades, he was one of 100 accepted on a defence engineering course. He studied subjects including electronics, mechanics and weaponry. He got up to work at 5am every day, and he says that he was proud to wear the uniform.

Still, the life he dreamed of was as a student, a life he was finally able to enjoy when sent to Moscow by the Burmese government in 2001. Later he returned to Burma as a production manager for the national nuclear weapons programme – his last job before he fled from the country for good.