Crossrail could swallow up another £1bn in funding and be delayed beyond 2019, ministers are expected to admit this week.

The flagship construction project to create a new high-capacity train line across London had originally been due to be opened on Sunday by the Queen, but problems with complex new signalling systems delayed testing trains in the central core. Confirmation that the opening was postponed by up to a year was only announced at the end of August.

According to the Financial Times, ministers could announce a further £1bn bailout for the scheme as early as Monday.

The resignation of chair Sir Terry Morgan last week – from both Crossrail and the next big British rail scheme, HS2 – has heightened speculation that further problems were yet to be disclosed.

City Hall and the Department for Transport (DfT) have been in continued talks with Crossrail to assess the full extent of the shortfall and delay. Twice already this year, the government and Transport for London have injected further funding, of £600m and a £350m loan, for a scheme long hailed as being delivered on time and within its £14.8bn budget.

The DfT has been keen to shift any further costs on to London, after growing political pressure about comparative transport spend in the north and south – with the transport secretary, Chris Grayling, expected to pick the lowest cost option for one of the most eagerly awaited rail upgrades in the north, the overhaul of the Transpennine route.

A DfT spokesperson said: “Constructive discussions between the government and Transport for London are ongoing on the terms of a longer-term funding and financing package for Crossrail, with London – as the primary beneficiary – bearing any additional costs via a financing arrangement. All parties are aiming to conclude these discussions as soon as possible.”

Meanwhile, the delayed opening of Crossrail – to be known as the Elizabeth line when operational – will exacerbate budgetary pressures on London. The city’s mayor, Sadiq Khan, confirmed a fare freeze for a third year last week, but revenues from Crossrail were expected to provide significant income next year.

A spokesperson for TfL said: “Everyone involved in this project is fully focused on bringing the Elizabeth line into service for passengers as soon as possible. Work is continuing between the government, mayor and Transport for London on finalising a financing package to deliver this.”

Tony Meggs, the chief executive of the Infrastructure and Projects Authority and a former BP executive, is being lined up as a possible chairman for Crossrail to replace Morgan, according to the Sunday Times.