Police said the raids were not connected to Lord Stevens' ongoing Quest inquiry into the Premier League and were 'totally independent'.
City of London Police would not disclose which clubs were involved, or their league status, but said search warrants were executed between 7.30am and 9am today.
A spokeswoman said: 'We can confirm that search warrants were served at three football clubs and the homes of two individuals in connection with corruption in football and its impact on owners and shareholders.
'This investigation is a totally independent inquiry.
'It has not been influenced or informed by the Quest inquiry in any way.
'As this is a live investigation, it would be inappropriate to comment further at this stage.'
Northumbria Police said all inquiries about today's football corruption raids were being handled by City of London Police.
But a spokesman for the North East force said they were aware that 'an operation' had been carried out earlier today by their London colleagues at St James' Park, the home of Newcastle United.