The EU said the Philippines must demonstrate audit are being carried out and that it has all the necessary technical and qualified human resources to monitor training institutions.
Deficiencies in audit and monitoring of maritime schools in the Philippines have yet to be fully addressed said the European Maritime Safety Agency (EMSA).
But the EMSA acknowledged progress made in raising the training standard of Filipino seafarers.
The EU demands Manila "provide by end of July 2014 the necessary evidence to demonstrate that all outstanding deficiencies have been resolved and that they have fully implemented the requirements.
Failure to live up to the United Nations International Convention on Standards of Training, Certification and Watchkeeping for Seafarers (STCW) may result in the loss of EU recognition, said the EMSA.
The warning comes after the European agency having found deficiencies in the way Filipino seafarers are trained. There are 100,000 Filipinos on EU-flagged ships.
The European Commission's Directorate General for Mobility and Transport presented to EU member states' its overall assessment of the Philippine maritime education, training and certification system in April.
"Philippine authorities have made efforts to bring their system in line with the requirements of the STCW," the EU said. "The efforts were supported by several EU member states, which provided technical assistance to Philippine authorities."