The fees included £252 to own a pet and £60 to put up a doorbell, it said.
Leasehold properties often require homeowners to pay ground rent and service charges for maintaining any common areas.
The consumer group said many leaseholders had made contact in recent months, reporting that they were often compelled to pay permission fees to freeholders and managing agents in order to be allowed to make home improvements.
Which? said the homeowners spoke of being forced to pay a fee of as much as £108 just to be permitted to file a request, followed by another fee to obtain the go-ahead to carry out the works.
It said it had received complaints from homeowners who were asked to pay as much as £2,500 to build a conservatory, £252 to own a pet, £60 to replace a doorbell and £300 to erect a fence.
One Which? reader feared her property was going to be repossessed after she built an extension and this concern was only lifted after she agreed to retrospectively pay a £1,600 fee, the consumer group said.
Which? also said that in an attempt to avoid paying ground rent, some homeowners had asked to purchase their freehold up-front.
Leaseholders told Which? they had however been discouraged to buy their freehold at the time of buying the property – only to discover later that the freehold had been sold on to a third-party company.
The consumer group said some homeowners could find themselves effectively “trapped” in properties they may struggle to sell on.
In December, the government announced a new crackdown on unfair leasehold practices – including making it cheaper and easier for existing leaseholders to buy out their freehold and better information available about redress for people who face the most onerous terms.
Which? money expert Gareth Shaw said: “We look forward to seeing firm action from the government to protect homeowners.”
The Home Builders Federation said: “Leasehold is in itself a secure and proven tenure that helps protect millions of homeowners.
“It works well for the vast majority of people who own their home with a lease in instances where they are interdependent and where facilities, grounds and services are shared by multiple households.
“The terms of leases should be proportionate and clearly communicated to buyers whenever they purchase a home.
“The industry continues to work with government and other stakeholders to ensure that leasehold terms are fair and transparent, providing confidence to homebuyers and existing leaseholders alike.”