Kiribati, Sierra Leone and Trinidad and Tobago each risk being listed as "uncooperative" in the fight against illegal fishing.
If identified issues are not resolved within six months, the EU can consider taking further steps, including trade sanctions on fisheries imports.
At the same time, the Commission has agreed to remove trade measures off Sri Lanka as it says it has "significantly improved" its national fisheries governance.
On Thursday, European environment, maritime affairs and fisheries Commissioner Karmenu Vella said: "Today's decisions are yet another sign of the EU's determination to fight illegal fishing globally. It also shows that we can bring important players on board: Sri Lanka has now a robust legal and policy framework to fight illegal fishing activities."
The official added, "As the fight against IUU fishing is part of the EU's commitment towards sustainability and good ocean governance, each third country that comes on board is an asset."
The EU's warning to Kiribati is based on concerns about the country's capacity to control fishing activities by foreign fleets.
It says there are "serious risks" that illegally caught fish could be laundered through the ports of Kiribati, as they do not have "robust" traceability systems in place for fisheries products.
The Commission said that Kiribati's "unwillingness" to share important information on third country vessels operating in their waters "undermines" EU work to improve transparency and sustainability of tuna resources in the western and central Pacific.
In a statement, the Commission said, "In Sierra Leone legal texts governing fisheries are outdated and sanctions fail to deter illegal operators operating internationally under the flag of Sierra Leone, without the fisheries authorities' knowledge. In addition, the number of licensed vessels exceeds the available resources and authorities fail to monitor or control their waters.
"Trinidad and Tobago also has a large fleet operating internationally where authorities do not control or inspect foreign vessels, nor cooperate with relevant flag states. The poor traceability system also causes the risk of laundering of fisheries products."
The executive has now proposed a "tailor-made action plan" that will help put in place what it calls "robust fisheries management control systems" for these countries.
However, the Commission says Sri Lanka has now successfully reformed its fisheries governance system.
It joins the growing list of countries (Ghana, Papua New Guinea, Korea, the Philippines, Fiji, Belize, Panama, Togo and Vanuatu) that have reformed their systems, following a warning by the EU.
Elsewhere, a yellow card, or warning, which was issued to Thailand last year will remain in place.
Bangkok was given an action plan to address shortcoming and the Commission is currently evaluating progress.
A Commission spokesperson said, "The dialogue is proving difficult and there remain serious concerns about the steps taken by Thailand to fight IUU fishing activities. This means that further action by the Commission cannot be ruled out."
She added, "A meeting with the Thai authorities in May will be a new opportunity for them to show their good will and commitment."