There were 52,746 complaints about mortgage businesses in the second half of 2011, up from 29,917 in the first half of 2011.
Some 47% of complaints – 25,687, were upheld in favour of the consumer, compared to 45% in the previous half of the year.
In total, mortgage firms paid out £44.4m in redress in the second half of the year, compared with £22.2m in the first half of the year.
Mortgages businesses are made up of home finance administrators, brokers and lenders.
The most common cause for complaint was related to the advising, selling and arranging of products,
Meanwhile, complaints about home finance products, which include equity release, impaired credit mortgages, and other regulated and non-regulated mortgages, stayed static at 69,088, compared to 67,537 in the first half of the year.
Santander UK received the most complaints relating to home finance products with 10,874, closely followed by Bank of Scotland with 10,034.
Other lenders with a large number of complaints include Barclays Bank, HSBC, Northern Rock (Asset Management), NatWest and Nationwide Building Society.
Overall, the FSA figures show the number of complaints about financial firms increased by 21% to 2,256,172 in the second half of 2011.
The main driver for this increase was a rise in the volume of complaints about general insurance and pure protection which increased by 49% to 1,280,940.
Most notably within this product group were the number of complaints about payment protection insurance which rose by 85% to 977,510.