The Spanish authorities said on Saturday that they were installing a floating barrier near a sea wall between Morocco and the autonomous city of Ceuta, after a surge of tens of thousands of migrants into the territory two days ago raised questions about Spain’s ability to control its borders.

The announcement, from Spain’s Interior Ministry, came as a vast majority of those migrants — most of them young Moroccan men seeking work — appeared to have left the city, a Spanish exclave in North Africa. For those who have stayed, and who have tried to evade the police and angry crowds of locals, the next steps remained unclear.

At least 48,300 of the roughly 50,000 to 60,000 people who had entered from Morocco had returned there by late Friday afternoon, according to Spain’s Interior Ministry, while hundreds more continued to leave throughout the night. A spokesperson for Spain’s government in Ceuta said at least 67 people had died trying to enter the city in recent days.

In Ceuta on Friday, Prime Minister Pedro Sánchez of Spain announced that the country would install buoys to “create a containment barrier — a physical barrier, if only a visual one” to strengthen the border.

The buoys will also comply with a recent ruling from Spain’s Supreme Court that had prompted the influx of migrants this week, Mr. Sánchez said.

Mr. Sánchez blamed human traffickers for spreading misinterpretations about the ruling, which said that migrants intercepted at sea could not be immediately sent back unless they had bypassed a barrier while trying to reach Spanish territory.

The new structure is a 500-meter-long inflatable barrier extending as much as one meter below the surface, the Interior Ministry said in a statement. It will be reinforced by an outer line of anchored buoys provided by the Spanish Navy, the ministry said.

Mr. Sánchez’s critics on the right, who have seized on the crisis to portray him as incapable of controlling the border, have called the measure inadequate.

“You don’t secure a border by putting buoys in the sea,” Alberto Núñez Feijóo, the leader of the conservative Popular Party, the main opposition group, said on Friday.

Although most of the migrants who arrived this week left Ceuta shortly after entering, questions remained about the fate of those still in the city.

On Friday evening, Spanish police officers, with their truncheons drawn, urged migrants to return. While most complied, others, especially the youngest, tried to evade the police. Some young Spaniards, angry over the authorities’ handling of the crisis, decided to take matters into their own hands and formed groups to intimidate the migrants.

On Friday night, a group of at least 50 young Spanish men swarmed into Plaza de los Reyes, in the city center, shouting, “To Morocco!” at several migrants resting there. A couple of the migrants fled, and the men chased them, nearly setting off a fight.

Some of the men intimidating the migrants wore face coverings, and the group clapped each time it managed to force a migrant to move. As the men marched down the street, they shouted, “Long live Spain!”