The situation at Sixfields has developed quickly since reports surfaced on Monday morning that the South London club were keen on talking to the man who masterminded Northampton's League Two title success and ensured they would be playing in the same division as Charlton next season.
Mr Thomas confirmed on the official NTFC website that he had given permission for talks to take place but wants a quick decision from both parties with the champagne having barely been drunk to celebrate Town's promotion.
He said: "We have a very strong, stable club with an excellent group of players, and it will be a very attractive job," said the Northampton chairman.