Michael Moller, the director-general at the UN's European headquarters, defended staff carrying out their second work stoppage this month, and criticised the manner in which the deductions were decided.
It was not immediately clear how many of the roughly 9,500 UN staff members in Geneva joined the strike against a 3.5 percent pay cut that is expected to swell to over five percent by June.
Smatterings of employees were outside the various entrances to the UN's compound in the Swiss city, brandishing red banners reading "UN staff in Geneva on strike."
A few hundred others gathered for a rally within the grounds, hoisting signs that declared "no confidence" in the International Civil Service Commission (ICSC), the New York-based body that imposed the cuts.
Moller agreed that the ICSC -- which calculates UN staff salaries across all duty stations including cost of living adjustments -- needed a shakeup.
"Listen, this is a body that has existed for a very, very long time and hasn't been reviewed in a long time ... the reality of the world and at UN has changed," he told reporters.
He underscored that the ICSC "is not supposed to be a cost-cutting machinery," but a technical department that calculates wages.
Union leaders insist the commission used faulty methodology in their recent cost of living calculations that triggered cuts in Geneva as well as steeper deductions in other duty stations, including Tokyo and Bangkok.
Moller warned the UN's "competitiveness on the work market," was going to suffer.
"It is a question of trust," he said.
He also rejected suggestions that he had personally tried to intimidate staff against striking.
"I am not in the business of intimidating my own staff," he said, but clarified that he warned workers that their pay would be docked for time absent.
Prisca Chaoui, executive secretary of the Coordination Council of the UN staff in Geneva, insisted the strike was not over the loss of "a few hundred francs."
"We're fighting for a principle we really believe in," she told AFP.
UN operations in Geneva appeared to be running on Friday, including the final day of the Human Rights Council session, which was proceeding following a deal with translators who had joined a previous strike.