Customers who can afford to restart repayments, should do so, the regulator stressed.
Borrowers have until 31 October to apply for a payment holiday. The current ban on lender repossessions of homes will also be continued until this date.
Payment holidays will not have a negative impact on credit files calls from lenders and other bodies to allow credit reference agencies to mark borrowers who have taken a second mortgage payment holiday.
Nationwide Building Society was among the most outspoken lenders with chief executive Joe Garner calling for records to include a notification.
However, lenders may factor payment holidays into future lending decisions after using information obtained from other sources, such as bank accounts.
Banks and building societies are to contact customers coming to the end of repayment holidays to offer a range of options on how missed payments will be repaid, in the cases where they are able to resume payments.
Borrowers still struggling may be offered further information on debt advice, as well as a range of options including part repayments or another three months break.
The guidance comes into force from 4 June.
Three-month mortgage payment holidays were available to homeowners from March as the country was put into lockdown.
More than 1.8m payment breaks were taken up.
Christopher Woolard, interim chief executive at the FCA, said: “The measures we have confirmed today will mean anyone who needs to can get help from their lender, if they are still struggling to pay their mortgage due to coronavirus.
“It is important that if a consumer can afford to re-start mortgage payments, it is in their best interests to do so.
“Customers should talk to their firm about the best option available for them.”