Ms Kelly said: "Today, as a country, we are faced with an unprecedented growth in people's desire to travel.
"It's essential that we provide people with greater choice over how and when they travel, cut congestion on our roads and take the right decisions for our quality of life, the environment and the long-term health of our economy."
The leader of Manchester City Council, Richard Leese, earlier told the BBC that fewer than 20% of motorists in Greater Manchester would have to pay the charge.
And he said the scheme would be of great benefit to more than 30% of households who relied entirely on public transport and currently struggled to get to work.
But Ms Villiers asked Ms Kelly: "What guarantees have people got in Manchester that there won't be excessive increases in the charge in the future?
"Has extending the congestion charge to a third outer ring been ruled out?"
Ms Villiers said three out of 10 local councils in Greater Manchester opposed the plans, and insisted there should be a conurbation-wide referendum.
The transport secretary has announced government backing for the plans
"The truth is the government is telling Manchester: 'If you say 'yes' to congestion charging you get money to improve transport. If you say 'No', you do not.
"That is bullying, pure and simple."
Opponents have pointed out that the scheme could cost motorists up to £1,200 a year at a time when fuel prices and road taxes are rising.
A spokesman for Manchester Against Road Tolls said: "Everybody would like to see improvements to public transport but people do not want a road tolls scheme with the less well off drivers forced off the road."
The Association of Greater Manchester Authorities (AGMA), which has proposed the scheme, said no congestion charge would be brought in before "significant improvements" had been made to bus, tram and rail services.
However, Stockport, Trafford and Bury councils are no longer supporting the bid for funding and councillors in Bolton have promised to hold a public referendum on the issue once all the facts are available.
The proposed public transport improvements would include:
• Metrolink extension to Rochdale and Oldham town centres, Ashton under Lyne, East Didsbury, Manchester Airport and the Trafford centre
• Second Metrolink route across Manchester city centre
• Priority for buses on several major roads
• Extra carriages for rail services
• Stations including Bolton, Salford, Altrincham, Stockport, Ashton and Rochdale, to become "interchanges", linking into other types of transport
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