Chakraverty took over Jackson's supervision of thyroxine use in 2011 at a time where her levels were variable, which had led her GP to prescribe 250mcg of thyroxine per day, which was intended to be for a short period.
When Chakraverty took over, he lowered the levels to 225mcg per day and later to 200mcg per day - but for two years. Jackson then continued the dosage for an additional year because no one told her to stop.
Dr Nicky Keay, a sports endocrinologist at Durham University, said: 'A high dose for a slim young person with accompanying report of significant symptoms is potentially suggestive of over replacement.'
Over the next two years, Jackson's health, mental state and training deteriorated to such an extent that Barry Fudge, now UKA Head of Endurance but then a sports scientist with the English Institute of Sport, asked her father if she had an eating disorder.
Her body fat was 9.5 per cent and skin folds were 35mm in March 2013, causing one nutritionist to comment she was 'the leanest female 800m runner he has ever encountered.'
She ran her personal best in early 2012 but failed to make the London Olympic team that year, after suffering a rib stress fracture and losing form.
During that period, Jackson says she was experiencing personality changes, becoming obsessive about food and training, constantly eating but always hungry. 'I was just training all the time and I was always hungry.
You know when you have to eat because you're so hungry? It was like that all the time. It wasn't a nice feeling. I was obsessed with what I was eating.
'I was looking at people around me thinking, why am I eating so much? You feel like your heart rate is always going and you can never switch off.
'Everyone thought the obsessiveness and personality change was down to missing out at the Olympics. Because I was so disappointed, people thought I had become obsessive. But it was actually because of the high dose. And as soon as the dose was brought back down my personality was visibly different.'
Keay said: 'High levels of thyroxine can lead to the situation of metabolism speeding up, causing adverse physical and psychological effects such as fast pulse rate, excessive hunger and compulsion to over exercise due to anxiety.'
Despite the warning signs and seeing her fat test results, Chakraverty continued to email her to say that she should 'stay on same dose of thyroxine.'
Jackson initially spoke out in 2015 about what she felt had been inappropriate care and at that stage UKA organised a meeting with her and Chakraverty to reassure her, at which she accepted that she had not been used as a guinea pig to test how effective thyroxine was.
But Jackson feels that she wasn't taken seriously by the endocrinologist at the meeting, Dr Kristien Boelaert, when suggesting that her stress fractures could have been caused by high doses of thyroxine
Jackson said: 'I am concerned how quickly I was dismissed in the meeting. They didn't seem to care about the fact that I was not able to eat enough to fuel my training. I explained why I felt let down but she [Boelaert] kept saying: "No, no, that's not the case. That wouldn't have caused stress fractures".'
'Before the meeting I could tell Rob [Chakraverty] was worried. After it had finished, he seemed relieved. I felt like I was coerced into getting the reaction they wanted about the causes of my injuries.'
After meeting with UKA, Jackson agreed to make a statement that she had accepted their reassurances 'that there was no attempt to boost my performance.' Also, Chakraverty denied that the high levels of thyroxine prescribed were to enhance performance.
However, contemporaneous notes taken at the meeting, seen by The Mail on Sunday, record that he did say he should have handled the case differently and that he apologised to Jackson.
Despite feeling undermined by Boelaert at the meeting, Jackson took up an offer to be assessed by her, after which the athlete said the doctor's attitude changed and she was 'really nice' and helped her regulate her dose.
'Running is repetitive so foot stress fractures are not unusual. Stress fractures in unusual areas would be clinically significant and further investigations warranted to identify the cause.'
Jackson had a stress fracture of the rib in June 2012, a fracture of the foot in July 2012 and two femur stress fractures in 2014. Boelaert declined to comment, citing patient confidentiality.
Last month Jackson was contacted by UKA, for the first time in five years, in the run up to the Panorama documentary, to remind her of the statement she had made in 2015. 'That was the first contact I've had in years and though it appeared friendly it felt like a threat not to speak out,' she said.
Keay said: 'In keeping with official guidelines from The National Institute for Health and Care Excellence (NICE), over treatment with thyroxine is indicated in the clinical context of significant symptoms and by suppressed levels of TSH (thyroid-stimulating hormone).
After Jackson's case, Chakraverty continued to suggest screening elite athletes for thyroid issues. The Daily Mail has documented how he raised the issue with Premier League doctors, discussing if it would be possible to screen England players for thyroid conditions, though they never did so due to the negative response he received.
He attended a summit with the English Institute of Sport in 2014 which discussed treatment of athletes for 'subclinical hypothyroidism' - essentially athletes on the borderline. Minutes from that meeting do, however, stress that it would not be administered as a performance-enhancing strategy.
Chakraverty said: 'I have had the privilege of working with many world-class athletes and I take pride in the care I provide, which is always in their best interests. I refute any suggestion that I have been encouraging medical screening or the use of medication for any reason other than protecting athletes' health.