A spokesman for the firm denied that Kojo Annan had ever touched contracts related to Iraq, or was involved in the scandal-plagued scheme.
The denial on Wednesday came after the United Nations confirmed on Friday that Kojo kept receiving payments from Geneva-based Cotecna until February 2004, years later than had been earlier reported.
The firm had obtained several contracts from 1999 to 2003 to inspect the imports of products to Iraq under the UN's oil-for-food programme.
Kojo Annan, employed at first as a trainee and then as a consultant, "was not involved in that contract nor in its implementation," the spokesman for Cotecna, Seth Goldschlager, said.
The UN secretary-general's son was employed in western Africa "in order to develop our businesses in Ghana and Nigeria", countries where he possessed dual nationality, the spokesman said.
Kojo Annan left the company when his contract expired at the end of 1998, signing a "no competition" deal in which he promised not to work with any of Cotecna's clients, added Goldschager.
It was under this agreement that the former staffer continued to be under Cotecna's payroll until the start of this year.
US investigators say UN officials
are among those who took bribes
"Such compensation is required under Swiss law," the spokesman explained.
The United Nations' oil-for-food programme allowed Saddam Hussein's government to sell oil under UN supervision in order to buy supplies to offset the effect of international sanctions on ordinary Iraqis.
But US investigators believe the Iraqi government may have siphoned off billions of dollars from the programme and allegations are swirling that UN officials were among hundreds of governments and officials to receive bribes.
The US daily, New York Sun, reported that Kojo Annan received $2500 monthly payments, while the Swiss economic daily Agefi estimated that the businessman earned $125,000 over five years.
The newspaper added that Annan junior had been "nicely rewarded" after having cheated with his expenses.
'Storm in a teacup'
Kofi Annan said on Monday that he was "disappointed and surprised" following the new revelations about his son's payments.
As for its work in Iraq, Goldschlager said he was "100% sure that all the questions concerning Cotecna will be lifted" concerning the oil-for-food inquiry in which the firm supplied "precise information in its possession".
Cotecna's work was mainly limited to customs on the documents provided by transporters, the spokesman insisted.
Annan said he was disappointed
and surprised by the revelations
"Cotecna had absolutely no role in the financial management of neither the programme nor any connection to the funds that were disbursed under the programme," he said.
He added that he regretted the "storm in a teacup which had been created that was damaging for the company".
A US senator heading a panel investigating the oil-for-food scheme called for the secretary-general's resignation in a Wall Street Journal opinion piece published on Wednesday.