Austria and Western Balkan states agreed on Wednesday to dispatch police forces to border zones to slow the flow of migrants along the Balkan route.
Interior and foreign ministers from ten countries meeting in Vienna also agreed to develop a unified criteria for the registration and deportation of migrants.
Austrian Foreign Minister Sebastian Kurz said there needed to be an end to the "waving through" of migrants on a quick path to Central Europe.
Ministers from Austria, Albania, Croatia, Bosnia and Herzegovina, Bulgaria, Kosovo, Macedonia, Montenegro, Serbia and Slovenia, had met with the purpose of working out a unified position on migrant flow ahead of Thursday's meeting of EU interior ministers in Brussels, an official close to the talks told dpa.
Greece sent a protest note to Vienna, complaining that the assembled ministers are failing to consult Athens.
Kurz defended the meeting in Vienna against criticism from Greece, saying: "I don't think there's a lack of collective meetings in Europe. It is the desire to reduce the flow of migrants that is missing."
Austria put in place daily entry quotas for refugees late last week, triggering restrictions in countries along the Balkan migration route, all the way back to the Greek-Macedonian border.
The European Commission has also criticized the restrictions as unlawful and running counter to an EU-wide approach.
Macedonia's new policy of denying entry to Afghans - one of the major migrant groups - has already caused a large backup on the Greek side of the border.
Serbian Interior Minister Nebojsa Stefanovic warned against the isolation of Greece through border barriers. "Without Greece it is impossible to have a joint solution," he told the Tanjug news agency.
Stefanovic questioned Austria's decision to cap the number of asylum seekers it will take at 80 per day and to allow transit at 3,200.
"The question isn't if we let more or less than 3,200 to pass, it is what if we let someone through, and then Slovenia and Austria turn them back, what do we do with them then?"
Another large group of migrants arrived in Athens' Piraeus port Wednesday morning, as thousands crowded the capital and roads leading north toward the Macedonian border.
Around 1,700 people arrived on ferries from Aegean islands Wednesday morning, bringing the total to around 9,000 over three days.
Hundreds spent the night in the open in Athens' central Victoria square, while thousands more stood or walked along highways leaving the capital and Greece's second-largest city, Thessaloniki.
In addition to the crowded borders, Greece also faces enduring economic woes that led to a third international bailout for the debt-riddled country last year.