Greece wants EU help sending migrants back to Turkey
The minister's comments came a day after he shared this proposal with his German counterpart Frank-Walter Steimeier in Berlin, Greek news agency ANA and a ministry source said.
Frontex currently operates 15 patrol boats in the Aegean Sea, whose mission is to assist Greek coastguard in their surveillance and rescue operations.
The minister said Frontex should deploy about 100 boats in the narrow stretch of water separating Greece from Turkey, the main launching pad for 850,000 refugees and migrants who reached Greece's shores last year.
Greece has repeatedly called on Frontex to help send back people deemed ineligible for asylum in Europe, such as migrants from Morocco and Pakistan.
Athens also wants Ankara to be pressured into honouring repatriation agreements signed with Greece and Europe.
Kotzias' remarks came as Austria, Hungary and Slovenia put pressure on Greece to stop the flow of migrants and refugees through its territory.
Athens and EU powerhouse Berlin are in talks on the migrant crisis - Europe's worst since World War II.
The focus of these talks is not to stop the flow of refugees, but rather to manage it better.
On Friday, at least 44 people including 20 children died after their boats sank on their way from Turkey to Greece.
The Greek coastguard said they had rescued 74 people after two boats ran into trouble off the Greek Aegean islands of Farmakonisi and Kalolimnos in the early hours.
They recovered the bodies of 17 children, 17 women and 10 men.
At least 113 people have died in the Aegean already this year, according to the International Organisation for Migration.