The European Commission said it will increase audits carried out on non-EU countries by 50 percent over the next two years, to ensure products entering the 27-nation bloc comply with its standards.
Checks at European border posts aimed at verifying that inspections are in line with EU requirements will also go up 33 percent, the commission said.
A task force would be set up to make import controls more efficient, it added.
"The EU must ensure that any animal, plant or food product arriving from other countries meets our strict health and safety standards," said EU health commissioner Oliver Varhelyi.
Varhelyi said the measures were unrelated to the Mercosur deal, but would help with its "enforcement and the implementation".
The commission is hoping to have the agreement approved by member states by December 20 despite opposition from France.
The agreement to form a 700-million-customer free-trade area, the world's biggest, is a key pillar in Brussels' push to open new markets in the face of US tariffs.
But farmers, particularly in France, have raised concerns that they would be undercut by a flow of cheaper goods from agricultural giant Brazil and its neighbours if it enters into force.
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