The regulator published complaints data for the six months to December 2012 which showed the Spanish-owned lender was the subject of 14,080 complaints.
Bank of Scotland received 8,628 complaints during this period followed by Northern Rock Asset Management (NRAM) which had 8,312 complaints.
Barclays Bank and HSBC rounded off the top five for complaints in the home finance category, receiving 5,257 and 4,359 respectively.
Figures for the whole banking industry show 3,422,384 were made in the six month period, an increase of 1% on the first half of 2012. Barclays, Lloyds TSB and Bank of Scotland topped the charts for most complaints across all financial services products.
Of these complaints, 2,170,537 concerned the subject of payment protection insurance (PPI). This figure was up 5% on the previous six months and accounted for 63% of all complaints.
The total amount of redress paid in the second half of 2012 was £2,946m, a decrease on the £3,169m paid between January and June.
Martin Wheatley, FCA chief executive, said: “Greater transparency drives greater competition, and the publication of the complaints data lays bare the track record of the UK’s financial institutions when it comes to resolving customer conflicts.
“When I meet with the bosses of the financial institutions they frequently tell me that they don’t want to be at the top of the table, which means they strive to improve both their sales and complaints handling processes.
“Not only does our data help consumers compare and contrast their current bank or lender, but it also boosts competition among firms too.”