Ombudsman Emily O'Reilly urged Frontex to improve how it restrains deportees, to ensure timely medical examinations, and to better protect disabled people as well as women and children.
She called on Frontex to ensure that families with children and pregnant women are seated separately from other deportees.
"Everything has to be done to ensure respect for the human dignity of the individuals being returned," O'Reilly said in a statement.
She remains "unhappy with the refusal of Frontex to establish its own complaints mechanism."
Working with the 28 member states, Frontex sent back to their home countries 13,000 people aboard 267 flights between 2006 and 2015, according to the ombudsman's office.
But it said that "to date, three critical situations have been reported, including in relation to the use of force."
Her office said part of the problem was that member states had different rules on the use of restraint.
"We are all shocked by the tragedies of those thousands who have lost their lives in their attempt to cross the Mediterranean," O'Reilly said.
The European Commission, the EU executive, is due on May 13th to present a comprehensive migration policy after the worst migrant shipwreck occurred in the Mediterranean last month with the drownings of 750 people.
It will go before EU heads of government and heads of state at their June 25th-26th summit.