The rise is partly being caused by an increase in bonuses for AIM directors, which also increased from £50,000 to £52,681 over the year to April 2012.
The IDS research, taken from its annual report, Directors' pay in smaller companies: AIMs, Fledglings and SmallCaps 2012, also shows that AIM directors' pay has risen sharply over the past seven years, with total earnings for executives increasing by 58%.
AIM, formerly the alternative investment market, is a sub-market of the London Stock Exchange, allowing smaller companies to float shares with a more flexible regulatory system than the main market.
Editor of the IDS report, Steve Tatton said: "Shareholders are happy for directors to receive bonus payments if they are genuinely tied to strong company performance. The worry is if the high bonus culture exists without sustainable returns being created for investors."
He added: "The intense focus on the FTSE-100 in the debate over executive pay has meant that significant pay growth for directors of smaller companies has taken place under the radar.
"Smaller companies may have avoided the full force of the shareholder spring up to now, but their pay committees will want to make sure they achieve the right balance between setting appropriate rewards for their directors and investor interests."
The data was collected from annual reports and accounts from 252 companies from financial year ending April 2012.
