The ports are a major source of income for state governments
Venezuela's military has taken control of key airports and sea ports under the terms of a move rubber-stamped by parliament a week ago.
The move centralises the running of the country's main transport hubs.
President Hugo Chavez has pushed for the move, describing it as "reunifying the motherland, which was in pieces".
Critics of Mr Chavez say the plans are unconstitutional, but the National Assembly backed them a week ago, saying they would improve essential services.
State governments in Venezuela have controlled the country's most important airports, sea ports and major highways since a move towards decentralisation began some 20 years ago, the AFP news agency says.
Many of the facilities seized on Saturday have since then fallen under the jurisdiction of state governments often hostile to Mr Chavez.
Correspondents say the ports provide them with an important source of local revenue - and the removal of this revenue will now make the localities more reliant on central government funding.
Soldiers were dispatched to ports in three states governed by Mr Chavez's opponents on Saturday - Zulia, Carabobo and Nueva Esparta.
They were also moving into Anzoategui, governed by an ally.
Since the government lost a number of key seats, including the mayoralty of Caracas, in local elections last year, there have been regular clashes over jurisdiction between local mayors and the national government.
The latest change to the law came just weeks after Venezuelans voted for a constitutional amendment granting Mr Chavez and other elected officials the right to stand for election beyond the previous limit of two terms.
The socialist leader has indicated on several occasions that he intends to run again for office in 2012 and has talked of remaining in power until 2021.