BBC SPORT | Football | BBC & FA hold bung evidence talks
The undercover documentary featured allegations of bungs to managers and illegal approaches by clubs to players.
"The meeting was positive and constructive," said a BBC statement.
"The BBC emphasised that it is keen to help the relevant authorities with their investigations and a proper process has now been put in place."
The FA wants to see the BBC's files, and had earlier said it was "disappointed" not to have had "full co-operation yet".
The FA wants to see the evidence as part of its joint investigation with the Premier League.
On Friday it said: "We have put in another formal request (to the BBC) to supply all the information gathered.
"We are disappointed that we have not had that full co-operation yet."
On Wednesday, the day after the documentary was shown, the FA had asked the BBC to provide evidence "as a matter of urgency".
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That same day, BBC Panorama had said in a statement that it would cooperate with requests "from the relevant investigating authorities, in line with our normal processes and procedures in cases of this kind".
Under investigation by the FA and Premier League jointly are Chelsea official Frank Arnesen, Portsmouth manager Harry Redknapp, and Liverpool and Newcastle as clubs.
The FA alone plan to look into allegations made about Bolton manager Sam Allardyce, his son Craig Allardyce, Redknapp's assistant at Pompey at the time of the filming Kevin Bond, and the agents Charles Collymore and Peter Harrison.
Another agent, Teni Yerima, is licensed in France so the FA will pass any information about him to Fifa or the French FA.
Bolton manager Allardyce was at the centre of the programme, with Yerima and Harrison claiming they paid him bungs.
Allardyce denies ever having taken or asked for a bung and says he has told his lawyers to "take the appropriate action". Bolton say they will carry out a "thorough and robust investigation" into the claims.
In the programme Harrison also describes offering to pay money to Allardyce's son Craig, who Panorama claims received secret payments from agents during three transfer deals.
Craig Allardyce has since said he was exaggerating his own importance to the undercover reporter in order to attract opportunities. He denied any wrongdoing in his Bolton deals or in his relationship with the club.
Harrison, filmed making claims about paying managers, now says that was just pub gossip and banter and added that he will sue the BBC.
Redknapp was filmed talking about Blackburn defender Andy Todd, but denies his conversation amounted to 'tapping up'.
And Bond was secretly recorded admitting he would consider discussing receiving payments from a proposed new agency involving Harrison.
Redknapp told the BBC that he has never taken a bung and had given Bond no reason to think otherwise, while Bond says he is not interested in receiving bungs and has also announced plans to sue the BBC.
The documentary also showed Chelsea's director of youth football, Frank Arnesen, and officials from Liverpool, discussing their interest in signing Middlesbrough's youth star Nathan Porritt. Newcastle were also implicated in the programme.
Chelsea and Liverpool both deny breaking Football Association rules. Liverpool say they have taken legal advice.
The FA also wants to contact Blackpool chairman Karl Oyston, after he claimed to have been offered bribes, and leading agent Jon Holmes who said managers had asked him for bungs.