A spokesman for Transport for London (TfL) said it is determined to recoup the money from Transys, which manages the swipe card travel system. The two main suppliers in the Transys consortium are EDS and Cubic.
Nearly 50,000 passengers were overcharged on 12 July after an IT error corrupted nearly 70,000 cards.
TfL Commissioner Peter Hendy told the TfL board on 30 July the loss of revenue from the glitches was more than £1m.
The spokesman said: "He expressed his determination that Transys should pay for this, rather than TfL or the ratepayer."
TfL is now in discussions with Transys and is looking at its contract to see what provisions could allow TfL to recover the money.
The company said in a statement: "The loss of revenue from both incidents is more than £1m but TfL is determined that TranSys should pay for these costs rather than TfL or Londoners."
TfL terminated the contractafter the July board meeting. TfL said the decision was a cost-cutting exercise and was not related to the IT problems.