1, with different status. The position of directly affiliated institutions within the government is lower than that of ministries and commissions. The directly affiliated government agencies are not part of the State Council, so their chief executives can't attend the the State Council meeting unless they have special needs.

2. The appointment methods of department heads are different. The appointment and removal of ministers and deputy ministers of government departments must go through the National People's Congress and its Standing Committee. The central government (that is, the State Council) has the right to decide on its own the establishment of institutions directly under the government and the appointment and removal of leaders, without going through the National People's Congress and its Standing Committee.

3. Different functions. Directly affiliated institutions have independent powers and special responsibilities, and can issue orders and instructions to the outside world within the scope of matters in charge. Therefore, directly affiliated institutions can become the subject of administrative actions. However, government departments must set up other subordinate departments to complete corresponding administrative tasks, such as the State Oceanic Administration (managed by the Ministry of Land and Resources).