Two key figures in the conviction of the Lockerbie bomber were secretly given rewards of up to $3m (£1.9m) in a deal discussed by Scottish detectives and the US government, according to legal papers released today.

The claims about the payments were revealed in a dossier of evidence that was intended to be used in an appeal by Abdelbaset al-Megrahi, the Libyan convicted of murdering 270 people in the bombing of Pan Am flight 103 in 1988.

Megrahi abandoned his appeal last month after the Libyan and Scottish governments struck a deal to free him on compassionate grounds because he is terminally ill with prostate cancer. Now in hospital in Tripoli, Megrahi said he wanted the public to see the evidence which he claims would have cleared him.

"I continue to protest my innocence – how could I fail to do so?," he said. "I have no desire to add to the upset of many people I know are profoundly affected by what happened in Lockerbie. My intention is only for the truth to be made known."

The documents published online by Megrahi's lawyers today show that the US Department of Justice (DoJ) was asked to pay $2m to Tony Gauci, the Maltese shopkeeper who gave crucial evidence at the trial suggesting that Megrahi had bought clothes later used in the suitcase that allegedly held the Lockerbie bomb.

The DoJ was also asked to pay a further $1m to his brother, Paul Gauci, who did not give evidence but played a major role in identifying the clothing and in "maintaining the resolve of his brother". The DoJ said their rewards could be increased and that the brothers were also eligible for the US witness protection programme, according to the documents.

The previously secret payments were uncovered by the Scottish Criminal Cases Review Commission (SCCRC), which returned Megrahi's conviction to the court of appeal in 2007 as a suspected miscarriage of justice. Many references were in private diaries kept by the detectives involved, Megrahi's lawyers said, but not their official notebooks.

The SCCRC was unable to establish exactly how much the brothers received under the DoJ's "reward-for-justice" programme but found it was after Megrahi's trial and his first appeal in 1992 was thrown out.

A memo written by "DI Dalgleish" to "ACC Graham" in 2007 confirms the men received "substantial payments from the American authorities".

The inspector claims the rewards were "engineered" after Megrahi's trial and appeal were over, but said there was "a real danger that if [the] SCCRC's statement of reasons is leaked to the media, Anthony Gauci could be portrayed as having given flawed evidence for financial reward." Instead, he claimed, the reward was intended to ensure the Gaucis could afford to leave Malta and start new lives "to avoid media and other unwanted attention".

However, the documents disclose that in 1989 the FBI told Dumfries and Galloway police that they wanted to offer Gauci "unlimited money" and $10,000 immediately. Gauci began talking of a possible reward in meetings with Dumfries and Galloway detectives in 1991, when a reward application was first made to the DoJ.

The evidence, which was due to be heard by the appeal court next month, also discloses that Gauci was visited 50 times by Scottish detectives before the trial and new testimony contradicting the prosecution's claims that Megrahi bought the clothes on 7 December 1988 – the only day he was in Malta during the critical period.

In 23 police interviews, Gauci gave contradictory evidence about who he believed bought the clothes, the person's age, appearance and the date of purchase. Two identification experts hired by Megrahi's appeal team said the police and prosecution breached the rules on witness interviews, using "suggestive" lines of questioning and allowing "irregular" identification line-ups.

Two new witnesses also disproved the prosecution claim that Megrahi was in Gauci's shop on 7 December, his lawyers said. Gauci said the area's Christmas lights were not on when the clothes were bought. The current Maltese high commissioner to the UK, Michael Rufalo, then the local MP, told the SCCRC the lights were switched on on 6 December, raising further inconsistencies in the prosecution case.

It has also emerged that Scottish police did not tell Megrahi's lawyers that another witness, David Wright, had seen two different Libyan men buying very similar clothes on a different day; evidence that psychologists believe may have confused Gauci and again clouded the prosecution case.

Dumfries and Galloway police said only a court could properly consider this material, and supported previous criticism of Megrahi's decision to release his appeal papers by Elish Angiolini, the lord advocate. "We will not be taking part in any discussion or debate concerning the selective publications made by Mr Megrahi," a statement said.

"We have nothing more to add other than to echo the lord advocate's recent comments pointing out that Mr Megrahi was convicted unanimously by three senior judges and his conviction was upheld unanimously by five judges, in an appeal court presided over by the lord justice general, Scotland's most senior judge. Mr Megrahi remains convicted of the worst terrorist atrocity in UK history."

A spokesman for the US Department of Justice also refused to comment, since Megrahi had voluntarily withdrawn his appeal. He said: "None of the allegations in the SCCRC referral, or the grounds of appeal filed by Megrahi, were finally adjudicated by the Scottish High Court of Justiary (the appropriate judicial forum) because Megrahi withdrew his appeal before the court could rule. Consequently, the U.S. Department of Justice will not comment further on his aborted appeal."