The wealth manager was hit by 345 investment complaints, 100 more than Barclays, which came second in the list.
The latest complaints data showed that 83 per cent of complaints made about Towry during the past six months of the year had been resolved.
Of the 1,782 listed investment-related complaints in total, 831 related to leading high street banks or their subsidiaries.
Barclays Bank, which was hit this year with a £7.7m fine for flawed advice to clients over cautious managed funds, amassed 245 complaints – 288, including its subsidiaries – while Santander received 187 complaints.
Towry said the figures did not reflect efforts it had made to resolve the complaints, many of which were from former clients of Edward Jones, which Towry bought in October 2009.
“The integration of the two businesses has resulted in a number of clients wishing to transfer their assets to alternative providers,” the firm said in a statement.
“This has led to a number of client complaints regarding the extended transfer period, which we have worked hard to resolve. However, the numbers represent a very small percentage of our client base.”
Barclays’ global retail banking chief executive Antony Jenkins said: “Our customers can be reassured we are making progress and are taking action to address the reasons our customers complain.”