An EU official said talks will continue in coming meetings.
"We expect this announcement (from EMA) will have a direct and immediate impact not only on our national vaccination plans, but also in our citizens' trust in vaccines against Covid-19," Portugal warned in its letter to the ministers on Tuesday.
The EU is grappling with a slow vaccine rollout caused by supply problems and by repeated changes in the use of the AstraZeneca shot, which have increased vaccine hesitancy.
"Harmonization at an EU level will be essential to stop the spread of misinformation," the letter added.
"It is essential that we follow a coordinated European approach. An approach which does not confuse citizens, and that does not fuel vaccine hesitancy," EU Health Commissioner Stella Kyriakides told ministers at the meeting, according to her speaking points.
Different age limits
But EU countries are recommending different age limits for the use of the vaccine, even though EMA recommended none because of a lack of data warranting them.
Germany has limited the use of the AstraZeneca vaccine to people over 60 and high-priority groups, and the country's vaccine commission recommended that people under 60 who have had a first shot should receive a different product for their second dose.
France and Belgium said the vaccine should only be given to people aged 55 and over.
In Finland it is given only to people aged 65 and over.
Other EU countries have currently no limits on the vaccine.
At the start of the vaccine roll-out in late January, Germany and France recommended that the AstraZeneca vaccine should be given only to people under 65, and Italy and Spain initially advised it only for the under-55s because they deemed the trial data for elderly people to be insufficient.
The vaccine was also suspended for a short while in March in several EU countries after first cases of blood clotting emerged, despite a lack of causal connection to the jab.