Transport secretary, Chris Grayling has said that Transport for London is in 'deep financial difficulties' in large part due to the mayor's policy of a fare freeze and issues around Crossrail.
He was speaking to the Transport Select Committee as part of its inquiries into the disastrous timetable changes earlier this year.
Mr Grayling apologised again for the failure but ruled out a fares freeze in January to compensate passengers.
He said: 'You just have to look at Transport for London with their partial freeze. TfL is in deep financial difficulties at the moment and not simply because of the challenges over Crossrail. The problem with a fares freeze if you costs go up every year, if you continue to pay more to your staff, you build a long-term and growing underlying problem in your finances.'
Mr Grayling said that the month's free travel and delay repay compensation offered to those passengers impacted by the timetable failures amounted to around 10% of their annual travel costs.
Committe chair, Lilian Greenwood said: 'GTR bought out their liabilities through to September and therefore don't seem to have suffered as a result of their appalling perfomance during the intropduction of this new timetable.'
Mr Grayling said: 'I can assure we are looking very carefully at what we are going to do about GTR and the poor performance this summer. We are close to a resolution on that. At the moment it is a commercial negotiation. At the moment I have not ruled out any options, so it would be wrong to say we intend to take no action.'
A mayoral spokesperson said: 'Sadiq makes no apologies for freezing TfL fares for four years and introducing the unlimited Hopper bus fare after fares rose by 42% under the previous mayor.
'The fares freeze is helping protect passenger numbers on the TfL network - which are falling much faster across the rest of the UK - and pales into insignificance next to the £700m per year of Government cuts to the TfL grant.'