UNESCO has been at the centre of controversy, particularly in the United States, the United Kingdom, and Singapore. During the 1970s and 1980s, UNESCO's support for a "New World Information Order" and its MacBride report calling for democratization of the media and a more egalitarian access to information was condemned in these countries as attempts to destroy the freedom of the press. UNESCO was perceived by some as a platform for communist and Third World countries to attack the West. In 1984, the United States withheld its contributions and withdrew from the organization in protest, followed by the United Kingdom in 1985 and Singapore in 1986. Following the change in government in 1997, the UK rejoined; the United States rejoined in 2003. During this period, considerable reforms had been implemented in the organization.

These included the following measures: the number of divisions in UNESCO was cut in half, allowing a corresponding halving of the number of Directors — from 200 to under 100, out of a total staff of approximately 2,000 worldwide. At the same time, the number of field units was cut from a peak of 79 in 1999 to 52 today. Parallel management structures, including 35 Cabinet-level special advisor positions, were abolished. Two hundred nine negotiated staff departures and buy-outs took place from 1999–2003, causing the inherited $10 million staff cost deficit to disappear. The staff pyramid, which was the most top-heavy in the UN system, was cut back as the number of high-level posts was halved and the “inflation” of posts was reversed through the down-grading many positions. Open competitive recruitment, results-based appraisal of staff, training of all managers and field rotation were instituted, as well as SISTER and SAP systems for transparency in results-based programming and budgeting. In addition, the Internal Oversight Service (IOS) was established in 2001 to improve organizational performance by including the lessons learned from program evaluations into the overall reform process. In reality though, IOS's main tasks involve auditing rather than programme oversight; it regularly carries out audits of UNESCO offices that essentially look into administrative and procedural compliance, but do not assess the relevance and usefulness of the activities and projects that are carried out.

Programming coherence and relevance remains a challenge at UNESCO. One of the main reasons for this is that activities and projects can be identified and supervised by various services within the organization (divisions and sections based at UNESCO Headquarters in Paris, UNESCO regional and cluster field offices and international insitutes) with insufficient coordination between them.