The research said that it costs an average of £3 to park in Bolton town centre for three hours - the amount of time FSB said is required for a proper visit to do shopping and/or to visit leisure facilities.
It placed Bolton as the second most expensive town centre, just behind Salford.
Phil Thompson, the FSB chair in Greater Manchester said: "Some councils charge nothing to park, but at the other end of the spectrum it's £3.50 for three hours. For many people paying to park is just not an affordable option, and all too often shoppers will vote with their feet."
Bolton Council disputed the figures and said it does not actually operate any off-street car parks in the town centre and are only responsible for on-street car parking.
A council spokesman said: "Encouraging shoppers to come into Bolton is a priority for us.
"The data issued by the FSB does not paint an accurate picture of car parking charges in the town centre.
"Our prices are competitive with other authorities in the region. You can park on-street in Bolton town centre, for up to 10 hours for as little as £2.
"Free weekend and Bank Holiday parking is also available in three NCP multi-storey car parks - Octagon, Topp Way and Deane Road.
"Costs at the 14 surface level car parks operated by NCP vary with a range of rates flexible to match the need of shoppers - some of the car parks charge £2.50 for 24 hours parking, and Sunday parking is £1.50 all day."