The hikes are occurring in some boroughs that have signed up to the capital's Childcare Affordability Programme (CAP).
Denise Burke, head of childcare at the London Development Agency, said there was anecdotal evidence that some community nurseries and private and voluntary providers housed in local authority buildings had been faced with rent increases.
She said the LDA was planning to investigate further to see how widespread the problem is.
Ms Burke said there was a conflict within local authorities with 'asset management departments trying to bring in more money, and children's services departments trying to manage the childcare market'.
She added, 'For many community nurseries, their fee structure was based on peppercorn rent. There is a pull in local authorities - one area is trying to manage the purse strings and increase rent, and this is having a devastating effect on the childcare market.'
Westminster Children's Society is paying a rent of £69,000 a year for one of its nursery sites in Westminster. Another saw its rent doubled from £12,000 to £24,000 last year.
Chief executive June O'Sullivan, said, 'We charge a reduced rate for children in need, but the rent is the market rate. It's impossible to balance with the anti-poverty agenda. Another rent increase can make or break a community nursery.'
Meanwhile, Ms Burke confirmed the CAP programme would be rolled out throughout England and expanded in London.
She said, 'We haven't got the meat on the bones yet. The funding, shape and format of the scheme are still to be worked out.'
