However, she said there would be no "top-down" approach by Whitehall and no creation of "expensive quangos" in any transport authority reorganisation.
Currently, there are six ITAs covering England's larger city-regions, some of which benefited from devolved powers over transport investment announced in this summer's City Deals.
Eagle said a party policy review on transport had concluded that existing ITAs should "secure new powers, responsibilities and funding".
She said: "I want to see a future Labour government pro-actively incentivising other city-regions to create ITAs of their own, or Transport for London-style bodies, to operate under combined authorities where that's a model that's adopted locally.
"Our review has concluded there's a benefit to being able to make transport decisions at a regional level, but I'm not in the business of creating new tiers of politicians and expensive quangos and structures.
"We believe regional transport partnerships between exisiting transport authorities could provide an accountable level to which government can devolve transport powers, responsibility and funding."
Last month, the Department for Transport (DfT) said it would proceed with plans to devolve funding for major local transport schemes to new local transport bodies (LTBs) from 2015.
These LTBs, the DfT said, would be "voluntary partnerships of local transport authorities, local enterprise partnerships and possibly others".
Eagle criticised the government's decision to put LEPs "in the driving seat" because, she said, "they're not accountable" and in some cases "not coherent".
She said under Labour, ITAs would work in partnership with LEPs but elected local authorities would be "clearly in the lead because accountability to the public is important".
However, she acknowledged that if Labour got to power in 2015, the LTBs could already be up and running which would "have to be taken into account".
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