FOS data includes both the number of complaints received about individual businesses and the percentage of complaints upheld by the ombudsman service in favour of consumers.
The Bank of Scotland received 590 complaints relating to mortgages and home finance, with 47% upheld in favour of the consumer.
Santander UK received the second highest with 460 and 31% upheld in favour of the consumer.
This was followed by Barclays Bank which received 362 with 45% upheld in favour of the consumer.
On average 38% of all mortgage complaints were upheld in favour of the consumer.
Other lenders that appeared in the table include Northern Rock Asset Management, which received 212 complaints with 34% upheld in favour of the consumer.
Clydesdale Bank and Cheltenham & Gloucester both received 201 complaints, with Clydesdale upholding 89% and C&G 28%.
While Sesame received 76 complaints, with 17 relating to mortgages and 56% upheld, while Openwork received 57 with 23 relating to mortgages and 43% upheld in favour of the consumer.
Overall, during this six-month period, the ombudsman service received a total of 149,925 new complaints – an increase of 54% on the 97,237 cases received in the second half of 2010.
Of the data published, 98,632 cases related to Payment Protection Insurance. 93% of the total number of cases involved 157 financial businesses, out of more than 100,000 businesses covered by the ombudsman.
Lloyds TSB Bank received 19,569 complaints overall, with 16,695 relating to PPI, followed by Barclays which received 16, 864, 12, 862 of which related to PPI.
Bank of Scotland was the third most complained about firm with 13,021 complaints, 9, 945 relating to PPI.
Lloyds TSB upheld 84% of all PPI cases, with Barclays upholding 73% and Bank of Scotland 62%.
Natalie Ceeney, chief executive and chief ombudsman, says: “These latest figures show a significant increase in the number of new PPI complaints referred to the ombudsman during the first half of 2011. This period coincided with the time when most of the high street banks and some other financial businesses had put PPI complaints on hold, because of their legal challenge against the ombudsman service and FSA.
“As a result, complaints in this period about PPI were harder fought, and harder to resolve – particularly if we found in favour of a consumer. This data therefore gives only a partial view on the cases which we were working to resolve over this period.”