Challenged on the issue at First Minister's Questions, he told Liberal Democrat leader Willie Rennie to look at the widespread support for the appointment across the business community before criticising the move.
He also highlighted the fact that, in common with 80% of senior public sector figures entitled to bonuses under contracts dating back to the Labour-LibDem coalition at Holyrood, Lena Wilson had decided to forego that bonus.
"Lena Wilson has a contractual entitlement to a public sector bonus, a contractual entitlement because the contracts were drawn up in the years of the Labour and Liberal Democrat administration in Scotland, where they were commonplace to have bonuses in the contracts of the chief executive of Scottish Enterprise," he said.
"She has relinquished that right to a public sector bonus. It seems to me that is something Willie Rennie should support because it's in line with Government policy that we have been trying to eliminate from public sector contracts entitlements to bonuses."
But this did not satisfy Mr Rennie, who has led criticism this week of the decision by the board of Scottish Enterprise to give Ms Wilson permission to accept an appointment to Intertek's board, which will earn her £55,000 for around a day's work per month.
Mr Rennie said a former senior official at Scottish Enterprise sent him a letter expressing his anger at the appointment. He added: "Most people, perhaps not those on the SNP benches, would not accept that £55,000 for 12 days' work can be justified for someone who is already being paid £200,000 every year.
"I can't really believe that the First Minister supports this appointment. If he reverses this decision today, he'll get my support."
Although Intertek has received nine grants from Scottish Enterprise in the past, the agency has insisted that procedures will be in place to prevent any conflicts of interest after Ms Wilson joins the board.