The report, assessing air safety and security rules, follows the apparently deliberate crashing of Germanwings flight 4U 9525 in March.
It endorses the "rule of two", where there should never be fewer than two people in the cockpit.
And it proposes improved medical and psychological checks on crews.
Investigators say that 27-year-old German co-pilot Andreas Lubitz intentionally slammed the Airbus A320 into the French Alps, killing all 150 people on board.
French prosecutors believe he may have suffered from psychosis and had a history of severe depression, but concealed many of his problems from his employer, perhaps fearing losing his job.
"We don't know everything that happened in this tragedy but we know a certain number of causes and we thought we may not want to wait until the final report of the accident investigation to launch actions," Patrick Ky, executive director of the European Aviation Safety Agency (Easa), told Reuters news agency.
Easa has delivered six recommendations for action to the European Commission:
Investigators have concluded that Mr Lubitz was able to deliberately crash the plane because he locked his co-pilot out of the cockpit when he went to the toilet.
In the wake of the crash, many airlines adopted the "rule of two" in the cockpit, and in its report the EASA says this should be maintained and evaluated after a year.
The report questions the use of manual cockpit door locks - introduced to prevent planes being hijacked - but suggests the risks they pose should be mitigated by the "rule of two".
It says all pilots should undergo psychological evaluations, and the psychological part of existing medical assessments and training for examiners should be strengthened.
The results of national medical examinations should be shared in an EU-wide database, the report suggests - with regulations ensuring "that an appropriate balance is found between patient confidentiality and the protection of public safety".
The report also calls for random drug and alcohol tests, and a robust oversight of medical examiners in the field.
Airline crew need to face tougher monitoring, the European aviation safety watchdog has recommended in a report to the EU.