In a joint statement with London mayor Sadiq Khan, Grayling backed the £30bn line.
It would run from Wimbledon to Tottenham with branches at each end forming a north-south equivalent to the east-west Crossrail line due to open next year.
London business rates paid a share of the cost of the original Crossrail and if the new line goes ahead the rates contribution is likely to increase sharply.
The joint statement said: “While London has shown how it could pay for half of the scheme over its life, the mayor and transport secretary want to see how London could fund half of the scheme during construction.
“They agree on the need to ensure a funding package which works for both London and the rest of the country and recognises other priorities, but also delivers the new capacity and connectivity that London needs.”
Grayling added: “I am a supporter of Crossrail 2 but given its price tag we have to ensure that we get this right.”
Greater Manchester elected mayor Andy Burnham condemned the move as “outrageous”, arguing that London already received more than its fair share of transport investment.
He had already been angered by Grayling’s decision earlier this week to potentially downgrade electrification of the rail line between Manchester and Leeds, seen as a vital economic corridor for northern England.
In a statement Burnham said: “The electrification of the line across the north is critical to the delivery of [the] government's promise of a Northern Powerhouse.
“The north has suffered from a lack of investment compared to the rest of the country and has had to put up with second class transport for too long.”
Khan though has issued a report showing that London does badly when its transport investment is judged on a per passenger basis.
This found that London Bridge station alone on any given day has nearly double the number of passenger arrivals of all of Birmingham’s stations.
“When those figures are considered London has one of the lowest amounts of railway and road spending per user in Great Britain,” the mayor said.
His research showed there were some 1.5 billion railway journeys across Great Britain in 2015-16, of which 63.8% were in London.
Yet the amount spent per passenger journey in London was approximately £6.94, below the British average of £10.31.
Public spending on roads in London was £23,700 per million vehicle miles in 2015-16, again below a national average of £29,400.
Khan said: “London is often accused of taking a bigger slice of the cake when it comes to public spending on transport. However, the capital faces a unique set of challenges relative to other regions of the UK, particularly the immense level of demand placed on our transport networks.
“To compare transport spending in London with any other UK region is just not comparing like with like and this report well and truly debunks the myth that we receive more than our fair share.”
