A decision by transport ministers to phase in the introduction of a new rail timetable was one of the factors leading to major disruption on the network, MPs were told.
Outgoing Govia Thameslink Railway (GTR) chief executive Charles Horton told the Commons' Transport Select Committee that the process for approving the timetable became "extremely protracted and was complicated by a number of changes".
He said: "One of those changes was there was a decision taken to phase in the timetable and that was made at the end of October 2017.
"That was a decision made by ministers."
Mr Horton, who announced his resignation on Friday, claimed the effect of that policy was "not clearly understood in terms of its impact on Network Rail's processes".
He added: "The result was that, that combined with some challenges in getting the timetable established, meant that we were into April before we had the timetable finalised."
Asked if the situation would have been helped with the decision being made sooner, Mr Horton replied: "In any timetable process the earlier you make a decision on specification the better it is in terms of your ability therefore to establish the timetable effectively."
Mr Horton stressed that the phasing of the new services was "not the only issue we were facing", noting that the "slow pace" of getting the timetables finalised contributed to GTR's difficulties.
Hundreds of services have been disrupted since schedules were changed on May 20.
Passengers using GTR and Northern have been particularly affected, with some stranded on platforms for several hours.
In the first two weeks, the proportion of trains either cancelled or delayed by more than 30 minutes was 13% for GTR and 11% for Northern.
Both operators introduced temporary timetables on June 4, removing around 6% of daily services in a bid to boost reliability.