Mr Clarke, a barrister with the firm Cartwright King which worked on prosecutions for the Post Office, was presented with a transcript of a June 2013 phone conversation with the IT expert Gareth Jenkins.
Mr Jenkins had given key evidence in a number of prosecutions, including that of the West Byfleet Postmistress Seema Misra, who was jailed while pregnant in 2010.
The transcript confirmed that Mr Jenkins knew of two bugs in the Horizon system, and that he could not be sure there were not more, and that he must have known of them earlier because he had informed the independent investigators Second Sight that they existed.
He agreed with the barrister questioning him, Julian Blake, that his had been “quite a bombshell moment”.
A few weeks later Mr Clarke wrote the advice, which warned that Mr Jenkins had failed to disclose information “in plain breach of his duty as an expert witness”, and this put the Post Office “in breach of its duty as a prosecutor”.
A lawyer for Mr Jenkins told the BBC in March it would be “inappropriate” for him to comment ahead of him giving evidence to the Inquiry in June.
When he joined the Post Office in 2013, Mr Clarke asked for a copy of the Post Office’s prosecution policy – the rules by which they decided to mount the prosecutions which sent hundreds of postmasters to jail.
What came back was a “single A4 document, badly photocopied”, he told the Inquiry. “I can’t remember what it said, but it wasn’t a prosecution policy,” he said.
He proposed a revised version based on the Crown Prosecution Service’s policy, and was disappointed when what he called a “watered-down version” was adopted.
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