London's transport system is a "barrier to the growth" of the city, Transport Secretary Ruth Kelly has said.
London's rail projects are aimed at cutting pressure on the Tube
But Ms Kelly said the Crossrail and Thameslink projects, to cut pressure on the Tube, showed the government was "investing very significantly".
Other parts of England had also "done quite well" out of spending plans, she told the Commons transport committee.
Tory MP Lee Scott said commuters were frequently experiencing conditions "we wouldn't let animals travel in".
Ms Kelly said extra money allocated to London in the 2004 transport white paper reflected the fact it was "much more expensive" to carry out projects there.
When questioned about her experience of travelling around the city, she said: "I use the Tube at the weekend and I regularly use the public transport system."
She added: "I use the railway service frequently and I'm absolutely sure that sometimes that involves standing."
Ms Kelly was asked whether she would give up her ministerial car to reduce greenhouse gas emissions, to which she replied: "Quite frankly, I don't think it would be practical, but I've switched to a Prius, however."
Ms Kelly told the MPs that transport funding was strongly linked to the economic improvements it brought, adding: "It's pretty clear that transport is a barrier to the growth of London."
Mr Scott, Tory MP for Ilford North, in Essex, said: "Passengers are experiencing travelling conditions we wouldn't let animals travel in. Can you stop this occurring?"
'Largest in Europe'
Ms Kelly replied that the government was "clearly investing very significantly" in London
She said the £16bn east-west Crossrail scheme and the £5.5bn improvement project for the north-south Thameslink line were necessary.
These would "in due course be the largest building programme in Europe, possibly the northern hemisphere".
But Mr Scott said these would be finished a "number of years hence".
Work on Thameslink is due to be completed by 2015 and Crossrail services to start running by 2017.
Questioned about the situation in the rest of England, Ms Kelly said: "I would argue that the regions have done quite well out of the transport white paper."
Manchester Blackley's Labour MP, Graham Stringer, said: "I find that breathtaking... It really is saying black is white.
He added that the regions were "not doing well", with the funding gap with London "increasing on a per capita basis".
Ms Kelly, MP for Bolton West, said the government had simplified its transport strategy into three broad priorities: travel between cities; connections between the UK and other countries; travel and within cities.
This simplified "radical departure" from previous policy, she added.