These containers have been lying in several ports in Hai Phong, Ho Chi Minh City and Ba Ria - Vung Tau Province after the government banned the import of scrap last year.
A number of western countries ship trash mostly to developing Asian countries, which are now slapping bans on them.
The containers have used goods, scrap paper and plastic.
The ministry has asked the government to assign relevant agencies to classify the shipments and identify their shipping companies and countries of origin.
The ministry's waste management agency suggested that after the classification customs could auction the waste that could be used as raw materials.
The Ministry of Transport could then order importers to re-export hazardous materials and those failing to meet Vietnamese standards, it said.
In the event of refusal by importers, the government would destroy the shipments and refuse them future import permits, it added.
The environment ministry also wants to penalize companies and individuals violating waste import regulations and not re-exporting prohibited items.
These measures are part of a draft resolution by the ministry to respond to the increasing threat of Vietnam becoming an international dumping ground.
Other preventive measures include adoption of national standards for six categories of scrap, which include what kind of scrap are allowed to be imported and how they should be cleansed and sorted.
In the last few months ports have only allowed companies registered on E-Manifest - a server which records customs declarations, clearances and related documents, and having permits to import scrap.
Vietnam imported 9.2 million tons of scrap last year, up 14 percent from 2017, according to customs.