"France a year ago received a record number of asylum seekers", she said, referring to the 100,000 asylum requests received by the country.
Muscat told the Italian Prime Minister Giuseppe Conte that Malta was acting in full conformity with its global obligations in rejecting the ship.
The Aquarius and two Italian ships that took on some of the 629 passengers are expected to arrive in Valencia on Saturday night, weather conditions permitting, said SOS Mediterranee co-founder Sophie Beau, whose charity operates the aid ship.
Italy's far-right Interior Minister Matteo Salvini had suggested that a planned meeting between the leaders of the two countries should be cancelled if France did not issue an "official apology".
How Europe should share the responsibility of handling migrants trying to get into the bloc from war zones and poor countries, largely across Africa and the Middle East, remains a vexed question.
"So I ask President Macron to pass from words to action and tomorrow morning, welcome the 9,000 France promised to welcome as a sign of concrete generosity and not just words", Salvini said.
Migrants wait by trains bound for France at Ventimiglia train station.
Merkel has pleaded for more time to negotiate with her European partners on a common response ahead of an EU summit on June 28-29.
Salvini's League scored its best-ever result in March national elections, partly on pledges to deport hundreds of thousands of migrants and halt the flow of newcomers, and has formed a coalition with the anti-system 5-Star Movement.
Oxfam said France should immediately stop and adequately sanction the "illegal practices of the French police at the French-Italian border", ensure the right to seek asylum for all foreign children in French territory and take care of them according to the provisions of national, European and other global laws.
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The source added: "I don't know exactly when the move is supposed to happen, but it is being talked about as a permanent move". She spent five nights in a military hospital before returning to the White House on May 19 to continue her recuperation.
Returned migrants are often sent to the Roja Camp in Ventimiglia, an Italian town near the border with France.
Italian maritime vessels that have picked up Europe-bound migrants in the Mediterranean still are entering the ports; on Wednesday, an Italian coast guard vessel docked in Catania, Sicily with 932 migrants on board.
It also details how Italy's overstretched and bureaucratic reception system is leaving vulnerable refugees and other migrants living under the radar in unsafe conditions.
This week, Italian and Maltese officials denied entry for the Aquarius, a ship carrying more than 600 Libyan migrants.
Macron, in a late Wednesday phone call with Italian Prime Minister Giuseppe Conte, said he did not mean to offend "Italy and the Italian people", according to a statement.
If they want, we will help them.
The French government was more conciliatory Wednesday, when the Foreign Ministry said France recognized the burden Italy has carried.
Conte said he and Macron "agreed on the need to cooperate closely" on migration issues.
Mr Conte will have a working lunch with French President Emmanuel Macron focusing on the migration challenge.
In televised remarks from Valencia, where Calvo was co-ordinating preparations for the arrival, the deputy prime minister said authorities will examine case by case if the migrants qualify for asylum according to the country's regulations.