Transport Minister Theresa Villiers has said she will look for "value for money" in the £16bn Crossrail project.
The transport budget is not ring-fenced from cuts, she added, which could have a significant impact on projects like Tube upgrades.
Last week London Mayor Boris Johnson said the Abbey Wood and Maidenhead Crossrail branches may be threatened.
Ex-mayor Ken Livingstone said chopping the link to Abbey Wood, south-east London, would deprive poorer areas.
Extension 'not expensive'
Ms Villier's comments come ahead of the government's announcement on spending cuts totalling £6bn.
The 72-mile (116km) route, due to begin service by 2017, will connect Maidenhead, Berkshire, with Shenfield in Essex via the West End and Canary Wharf, with a link to Heathrow Airport.
Transport Secretary Philip Hammond has already said it may not be completed on time.
Ms Villiers told BBC1's The Politics Show: "We support Crossrail and work is already going ahead on it and it is vital we work with the mayor to look for value for money for this project.
"No decisions have been made on cutting scope."
"Its likely there will be some cuts [in the Department for Transport], that is not a department that has been ring-fenced."
Signed and sealed
Mr Livingstone said Crossrail was "crucial to the London economy".
"I think it would be a sadness not to do the extensions into the poorer parts of London because that allows people to get into the city and find work.
"The real expense is building the tunnel, the bit down to Abbey Wood is not the expensive bit," he said.
Last week the mayor warned that Abbey Wood and Maidenhead extensions could be under threat.
"They will come in and they would kick the tyres and say can we descope it," he said.
"We have got to make the case for getting on with that [Crossrail] project. But I do not want you to rush away with the idea that it's all signed and sealed. That's simply not the case," he added.
Transport for London has already said it is looking to make £5bn of efficiency cuts.