Kit Malthouse was speaking yesterday at a conference fringe event organised by think-tank Planning Futures on how local authorities can use planning to increase housing delivery.
Malthouse said the government had "recently" raised planning application fees and is "thinking about" the second rise in planning fees that it trailed last year.
An optional 20 per cent increase in application fees came into force earlier this year. But the government also announced, last September, that it was considering increasing fees in certain areas, where homes had been delivered to meet "community needs", by a further 20 per cent.
Malthouse also said councils can use planning performance agreements, which allow developers to pay for councils processing their applications in return for certain performance guarantees, such as on decision timescales.
Asked about whether authorities should be allowed to set their own fees, Malthouse said: "Having been a local authority member myself, I have a natural resentment towards central control of that kind of thing.
"Having said that, there is a worry that if local authorities were allowed to let rip with charges, that might exclude smaller developers that couldn't necessarily afford the charges that are required.
"We have to be slighly careful, particularly in a market where we are trying to encourage more new entrants to come in that we don't raise yet more barriers to entry.
"But I'm always happy to look at that. If it becomes clear that capacity in planning departments is really a constraint on development, then we may well have to do something about it, so we will keep that under review."
Also speaking at the event, Jonathan Layzell, executive director of housing association Stonewater, said developers would be prepared to pay more in fees for a better service.
He said: "We do recognise that the planning system is under-resourced. There's a lack of experienced planning officers.
"So planning applications that ought to take a little over three months from start to finish are taking 12, 18 or 24 months, or even longer.
"We need to invest in skills at a local authority level. I think the development industry can carry a share of the burden for that.
"The industry would be prepared to pay a bit more in fees if there was a direct relationship to the speed at which applications were dealt with and the speed at which we could get onto site."
Planning, in association with the Planning Officers Society, is currently carrying out a survey of the impact of the planning application fee rise and local planning authority resourcing levels.
Respondents, who must be senior managers in planning authorities, will be entered into the prize draw to win £100 of Marks & Spencer vouchers. For more details, and to submit an response to the survey, click here.
Last year, Planning published research into how planning authorities intended to spend the fee increase.