Football Association chief executive Brian Barwick today announced a formal investigation into the allegations made by BBC's Panorama programme.
Every agent, manager and club named by the programme for alleged wrongdoing will be investigated.
One probe relating to players' agents and connected activities will be carried out by the FA alone, and another investigation by the FA and Premier League jointly.
Barwick said: 'These are serious allegations which have been made by Panorama and we are determined to investigate them fully. It is vital for the integrity of the game and for every football supporter that we do this.
'We will work in close co-operation with the Premier League. As with any investigation, we will ensure that our inquiries are exhaustive and thorough. If we find evidence of corruption we will act on it.
'We recognise our responsibility.'
'Undercover: Football's Dirty Secrets' claimed that Bolton boss Sam Allardyce and his son Craig, until recently a football agent, were given illegal payments to facilitate player transfers.
The FA have asked the BBC to hand over all of the information Panorama obtained during their investigation 'as a matter of urgency'.
The FA alone will investigate the allegations about illegal payments made by the BBC against the Allardyces, Newcastle assistant manager Kevin Bond and agents Charles Collymore and Peter Harrison.
The joint FA/Premier League probe will cover allegations of illegal approaches involving Chelsea's head of development and scouting Frank Arnesen, Liverpool, Newcastle and Portsmouth manager Harry Redknapp.
Arnesen and a Liverpool official were filmed by Panorama discussing a deal for England youth player Nathan Porritt to leave Middlesbrough, and Newcastle were also alleged to have done so.
The joint investigation will also look into the transfers of Hidetoshi Nakata, Tal Ben Haim and Ali Al-Habsi to Bolton as these fall within the timeframe of the inquiry being carried out by Lord Stevens for the Premier League.
The FA said in a statement: 'The FA takes any allegations of corruption in the game extremely seriously and will actively investigate the claims made by the programme.
'Discussions have already taken place with the Premier League as to how these joint investigations will be managed.
'The FA will also speak to all other parties named in the programme. Based on the evidence obtained, The FA will then determine what action should be taken.'
The FA will also refer any evidence about French-licensed agent Teni Yerima to FIFA and the French.
The BBC have agreed to pass their evidence to the investigations.
The BBC said in a statement: 'The BBC will co-operate with requests relating to last night's Panorama `Undercover: Football's Dirty Secrets' from the relevant investigating authorities, and will do so in line with our normal processes and procedures in cases of this kind.'