Lena Wilson, who has a remuneration package of about £200,000 as chief executive of the publicly-backed enterprise agency, faced criticism when she joined Intertek as a non-executive director.
At that time, in July 2012, her basic annual fee for the role was said to be £55,000 for about one day of work each month. Now Intertek's annual report, published yesterday, shows that was increased to £58,000 last year
However, 50-year-old Ms Wilson picked up an additional £2583 through other work she carried out for the business in her non-executive role.
Intertek had initially published that Ms Wilson received total fees of £75,000 in 2013, but later confirmed that was a mistake. She is due to receive £68,000 this year.
The annual report notes she attended all seven of London-based Intertek's board meetings in the year.
It also points out that she joined the company's audit and risk committee in September last year and attended the two meetings held by that group in the final four months of 2013.
Members of that committee receive an additional £10,000 each year on top of their basic fees.
Michael Wareing, chairman of the audit and risk committee, said: "Lena brings with her a wealth of experience and she has already made valuable contributions since joining the committee."
Scottish Liberal Democrat leader Willie Rennie MSP said: "John Swinney should explain why the full-time head of a publicly funded body is working part-time for another organisation.
"I'm sure most people in Scotland would agree that such a handsome remuneration at £200,000 should command the full commitment of the person employed to the role."
Other non-executives who served at Intertek across the whole of 2013 were paid between £64,000 and £90,000, while chairman Sir David Reid received £340,000.
Chief executive Wolfhart Hauser received more than £3.2m while finance head Lloyd Pitchford was paid almost £1.7m.
Scottish Labour's deputy finance spokeswoman Jenny Marra said: "Commanding a high salary in the public sector is different from the business environment.
"As it's tax payers' money there is an expectation that the employee will be wholly devoted to their job with no other external responsibilities and interests.
"While it's vital that Scottish Enterprise directors have their finger on the pulse of business, I don't think it's the public expectation that highly paid public servants are pulled off in other directions. Scotland's economy needs its full-time officials doing their jobs full-time."
According to the annual report, Ms Wilson owns 154 Intertek shares and her basic fee will remain at £58,000 in 2014. The shares were worth 2943p each at the close of trading on the London Stock Exchange yesterday.
The annual report states: "Fees for the non-executive directors are determined by the board . . . Individual non-executive directors do not take part in discussions regarding their own fees."
Ms Wilson, who declined to comment, has been chief executive at Scottish Enterprise since November 2009 having spent much of her career working in economic development.