General Michael Lollesgaard confirmed in letters to Yemen's government and the Houthis that "since May 14, the Houthi military presence was not detected in the ports by regular verification patrols" carried out by the UN.
Lollesgaard asked the Houthis to remove "all military manifestations, including trenches" from Hodeida port, a key entry point for humanitarian aid to Yemen.
The rebel pullback from Hodeida, Saleef and Ras Issa last month marked the first concrete step to implement a ceasefire deal reached in Sweden six months ago.
The Huthis handed over control of the ports to a "coast guard," but Yemen's government said these forces were in fact rebel fighters in different uniforms.
Lollesgaard said in a statement that the Houthi pullout from the ports was "significant" and had transformed the ports into a "civilian space" for Yemen's port authorities to carry out their work, with UN support.
Under the Stockholm agreement, rebel fighters and government forces are to carry out a two-phase pullback from Hodeida and the ports, but negotiations are continuing on further redeployments.
The pullback from the three ports represent only part of the initial phase of the redeployment.
UN envoy Martin Griffiths, who has been sharply criticized by Yemen's president for his handling of the rebel withdrawal from the ports, is to report to the Security Council on Monday.
The conflict between Yemen's Saudi-backed government and Iran-aligned Houthis has killed tens of thousands of people and triggered the world's worst humanitarian crisis, according to the United Nations.