France and Germany would be "extremely insistent" on the need for control centres in Greece, Italy and Hungary "to prevent what is happening today", Hollande said on Monday.
He and German Chancellor Angela Merkel had discussed a common line for the meeting by phone on Sunday evening.
French Interior Minister Bernard Cazeneuve on Monday said that Germany was "not closing the door" to migrants but instituting identity checks to ensure that people entering the country have refugee status .
It would be "stupid" to impose checks on the Franco-German border, he added.
Merkel's spokesperson, Steffen Seibert, had the same message shortly afterwards, declaring that "temporary border controls are not the same as closing the borders".
On Monday Austria, Slovakia and the Czech republic said they would institute controls at their borders, while Hungary deployed soldiers at its frontier.
The Schengen free-movement agreement was effectively suspended by the moves.
Monday's meeting was to discuss imposing quotas to share out 160,000 refugees from Syria and north Africa on member countries.
Czech Prime Minister Bohuslav Sobotka has said his country will never accept compulsory quotas and Polish European Affairs Minister Rafal Trzaskowski warned Monday of an EU "institutional crisis" if quotas were imposed without all countries' agreeing to them.
"France will not accept that some countries, in exchange for a fine, leave the task of taking in refugees" to others, Cazeneuve told RTL radio.
Diplomats said that the EU on Monday approved military action, including stopping and destroying boats when deemed necessary, against people smugglers in the Mediterranean.
More than 350,000 people have crossed the Mediterranean this year and nearly 3,000 have died trying to do so, according to the International Organisation for Migration.