It comes as City Hall published figures it said showed Southern rail services were the worst in the UK.
Sadiq Khan also repeated his call for the government to give him emergency control of Southern services.
The government said it did not "routinely publish" official advice given by civil servants.
Earlier this month Transport Secretary Chris Grayling said the government would not devolve control of suburban rail services to TfL but that he wanted it to be "closely involved" in developing services.
That went against indications from his predecessor Patrick McLoughlin, who had earlier this year appeared to suggest services operated by Southern, Southeastern and South West trains could be devolved to TfL once their current franchises ended.
A spokesman for the mayor told the BBC: "Londoners deserve to know why the government has backtracked on their promise to give London control of services which would have led to fewer delays, a better service and passenger fares frozen.
"If the government really believes they have made the right decision, they should have no problem with publishing the advice as soon as possible."
On Tuesday, transport minister Lord Ahmad told the House of Lords the government would not publish the advice it received after seeing an advance copy of TfL's business plan in October.
He added the government's analysis "highlighted a number of uncertainties in the business case, particularly around the operational risks associated with splitting the franchise and around the benefits being claimed [by City Hall]".
But on Thursday the mayor repeated his demand that City Hall be given emergency control of the Southern Rail franchise as he published train punctuality figures he said both the government and Govia  - the owner of the Southern Rail franchise - should be "utterly ashamed" by.
The figures showed 57% of trains on Southern Rail's Mainline and Coast line arrived at their destination on time in the five weeks to 10 December.
The figures also showed 62% of trains across all Govia's franchises, which include Govia Thameslink train services and the Gatwick Express, arrived at their destination on time in the same five weeks.
That was the worst period of performance for any train operator since 2005, City Hall said.
It added not all of Govia's rail franchises had been affected by strike action and yet it ran five out of six of the least reliable train lines in the whole country and was missing its reliability target by 28%.
But a spokesperson for Govia said the punctuality figures reflected "the significant impact" of "wholly unjustified industrial action being taken by Aslef and the RMT".
They added ongoing additional knock-on delays were the result of continued work at London Bridge.
The spokesman said: "We're sorry - our passengers deserve better and, together with Network Rail, we're working hard to improve performance."
The DfT has previously said it is not within Mr Grayling's powers to strip Southern of its franchise.
Mick Cash, leader of the RMT union, which will stage another 48-hour strike on Southern Rail services beginning on New Year's Eve called the latest performance figures: "shocking and abysmal" and called for "the immediate sacking of Southern Rail".
"The fact that they still hold the contract despite plunging Britain's biggest rail franchise into total meltdown proves that they are being propped up by the government for political and ideological reasons. It is a national disgrace," he added.

The head of Madagascar's FA is the sole challenger to the Cameroonian, who has led Caf since 1988.
Central to Ahmad's manifesto is a desire for improved governance, with a commitment to increased transparency and reinvestment outlined.
The Ethiopian capital Addis Ababa will host the elections on 16 March.
Ahmad, who confirmed his candidacy to the BBC on 12 January, has also said he hopes to bring about 'reconciliation within the different actors of the African football.'
"Those who have lost their trust, their confidence in Caf, those who have been long forgotten and those who have been left on their own - they all must join Caf," his manifesto states.
Among the other ideas prominent to his candidacy:
Ahmad is seen as an outsider to depose Hayatou, who is seeking an eighth term in office, and is eligible to contest the elections given he is already a member of Caf's Executive Committee.
The Malagasy has been boosted by receiving the backing of Cosafa, the southern African region.
Ahmad is considered the most serious challenger in years to Hayatou, who was re-elected unopposed in 2013.
London's mayor has challenged ministers to publish advice they received over possibly devolving suburban rail services to Transport for London (TfL).
[NEXT_CONCEPT]
Ahmad Ahmad, the man bidding to depose Issa Hayatou as president of the Confederation of African Football (Caf), has unveiled his manifesto.