More than half (51%) of the 63,457 complaints made against investment products were upheld and £58m paid out in compensation, the data revealed.
The total number of complaints rose in the last six months of 2016 in the first release of the data since the FCA expanded its requirements of firms reporting the number of complaints.
The rise was expected as new rules introduced by the regulator in 2015 mean all complaints data is captured with firms given longer to deal with complaints informally.
The number of complaints stemming from investment products equated to around 2 complaints per 1,000 client accounts.
Investment ISAs received the most complaints, with 14,600 made while investment bonds received 9,300 complaints.
Unit trusts and Oeics received around 6,000 complaints and platform services were the cause of more than 5,300.
However, the total complaints about investments made up just 2% of the total 3.04m complaints made across insurance, pensions and banking and credit cards.
