The German city is one of 19 bids to host the EMA when Britain leaves the EU. Athens was primarily among them, before the government apparently changed its mind.
Eurocrats will have to lay off about 72 UK nationals working at the EMA because it can only employ people from member states.
Mr Katrougalos said the southern member states had been active in forming alliances, but admitted discussions could be “very difficult politically”.
But he said the Greek backing to move the EMA to Frankfurt is “complete” and has “good chances”.
Margarida Marques, the Portuguese State Secretary for European Affairs, said the bloc’s southern countries were better positioned to host the EMA.
She said: “Officials from the EMA prefer to go to the south more than the north because the weather and the food are better.
It comes as it emerged Britain is set to be slapped with a mammoth £521m bill to cover the cost of relocating the major EU agency from London to the continent after Brexit.
The Eurocrats’ estimated cost of moving the EMA out of the UK – including moving its operations and staff and paying off the remainder of a locked in lease that runs until June 2039 – is £163million above their initial estimate.