It said just 8% of councils had built enough to replace half of their stock sold through the scheme, which allows council tenants to buy their homes.
The charity said there was a danger of some areas having no affordable homes.
The government said it was committed to building 275,000 affordable new homes over the course of this parliament.
Right to Buy was first introduced in the 1980s under Margaret Thatcher's government and was given a boost in 2012 when discounts for tenants were increased to Â£75,000.
In this year's Queen's speech the government announced the scheme was being extended to 1.3m housing association tenants in England.
Shelter, which looked at provisional figures from the Department for Communities and Local Government, said just two of the 166 councils in England listed as selling properties through Right to Buy had succeeded in replacing more than 100% of the properties sold.
Under existing policy, the government has promised that each home sold after 2012 would be replaced.
The charity's chief executive Campbell Robb warned the problem of not enough council homes being replaced was only likely to get worse, leaving some areas with no affordable homes.
"At this rate they'll soon be black-spots across the country where no-one on a normal income can afford to live," he said.
1. North Kesteven 187%
2. New Forest 128%
3. Waverley 89%
4. Barking and Dagenham 88%
5. Winchester 81%
6. Ipswich 80%
7. Tandridge 79%
8. Castle Point 71%
9. Hounslow 64%
10. South Cambridgeshire 59%
The Local Government Association (LGA), which represents councils in England and Wales, said many council housing programmes were hampered by complex rules and restrictions on the use of receipts from sales of homes.
LGA housing spokesman Peter Box said: "It is imperative that councils are given the powers to replace housing sold through Right to Buy quickly and effectively as part of the Spending Review.
"Councils need to be able to retain 100% of receipts from sales while Right to Buy discounts should be set locally so they reflect the cost of houses in the area."
Mr Box said the LGA estimated this would allow councils to replace 50,000 homes sold over the lifetime of the next Parliament.
The government said nearly 40,000 new homeowners had been created since it increased discounts for council tenants in 2012.
A spokesman added: "Councils are continuing to fulfil the requirement to deliver one for one replacements within three years, and over 3,000 replacement homes have already been delivered across England.
"We have been absolutely clear that if councils do not deliver one for one replacements for the additional homes sold under Right to Buy the government will."
One in three councils in England has not replaced a single home sold through the Right to Buy scheme since 2012, according to the charity Shelter.