The main purpose of this research is focused on understanding the politico-administrative system and structure of rural policy implementation in the third programming period (2000-2006). Case studies have been conducted for selected measures of the Greek Rural Development Programme (RDP) and LEADER+ initiative. In-depth interviews were conducted with officials involved in the rural development policy implementation. Inflexibility due to centralization, lack of personnel motivation and inadequacy of the personnel involved in policy implementation are the main weaknesses. Work seasonal overload is also a weakness, which can be caused by peak periods or by too many and in part possibly unnecessary documents, official permissions and other legal or administrative obligations. The administrative personnel should be better motivated by financial bonus and properly trained. A central integrated database, accessible to all administrative levels and units, should also be designed. Such changes could lead to a smoother decentralisation process because in some cases centralisation is considered to cause communication obstacles, work overload and delays.