Speaking after talks in Vienna with leaders along the Balkan migrants trail into Europe, Merkel said the continent must "stop illegal immigration while living up to our humanitarian responsibilities".
To this end "it is necessary to get agreements with third countries, especially in Africa but also Pakistan and Afghanistan... so that it becomes clear that those with no right to stay in Europe can go back to their home countries," she told reporters.
Last year hundreds of thousands of people, many fleeing the Syrian war, trekked up from Greece through the western Balkans to northern Europe, in the continent's biggest migration crisis since 1945.
Populist parties across Europe have stoked concerns about the influx, not least Alternative for Germany (AfD), which has stolen support from Merkel's centre-right party in recent state elections.
On Monday Merkel said for the first time that the influx could have been better handled.
In March, under pressure from Austria, Balkan countries closed their borders, and the flow has since slowed dramatically, although 100-150 still make it to Austria every day, Vienna says.
The same month the EU struck a deal with Turkey -- home to more than three million refugees -- under which Ankara promised to halt the inflow in return for billions in aid and other sweeteners.
The pact may yet collapse, however, in the wake of the July 15 coup attempt in Turkey.
Greece under strain
As illustrated by a large fire at a refugee camp on the island of Lesbos on Monday, Greece meanwhile remains under severe strain, with more than 60,000 people stranded.
An EU scheme to relocate them -- and others in Italy -- around the bloc has failed to live up to expectations, while extra administrative assistance promised by the EU has been insufficient.
Merkel on Saturday said that EU countries' participation in the relocation scheme has been "too slow", saying this could "increase the pressure" on Greece's border with Bulgaria.
"It is unacceptable that the countries that first receive (the migrants) bear the burden," Greek Prime Minister Alexis Tsipras said in Vienna, according to ANA.
"This is also a question that concerns destination countries."
Bulgaria, the EU's poorest country, is home to around 10,000 stranded migrants although Brussels has promised Sofia extra support including help from a new EU border force from October 6.
'Closed for good'
EU President Donald Tusk, also in Vienna, said that it was necessary "to confirm, politically and in practice, that the western Balkan route of irregular migration is closed for good".
The difficulties of making it through to the Balkans is thought to be prompting increasing numbers to attempt treacherous sea crossings from Libya or Egypt to Italy instead.
More than 300,000 migrants have crossed the Mediterranean this year, the UN said on Tuesday. Some 3,500 have perished in the attempt. On Friday more than 160 drowned off Egypt.
Echoing Merkel, Hungarian Prime Minister Viktor Orban said Saturday that this showed that the EU needed to send people back to Egypt, Libya and other countries.
Orban, who has been scathing about Merkel's "open-door" policy and has called immigration "poison", has refused to take in a single migrant under the EU relocation scheme.
Attacks on asylum seekers
Meanwhile, attacks on centres for asylum seekers in Austria are on course to double this year, according to government figures released on Saturday.
Twenty-four were recorded in the first half of 2016, compared with 25 for the whole of 2015, Interior Minister Wolfgang Sobotka said in reply to a parliamentary enquiry.
The incidents ranged from arson to acid attacks to stones thrown through windows, or racist or Nazi graffiti and hate postings on the Internet.
Opposition Green MP Albert Steinhauser, who made the enquiry, blamed the rise on the "heated political debate about asylum seekers."
"If in politics there is an atmosphere of intolerance... then it's no wonder that some people see such attacks as legitimate," Steinhauser said.
Austria saw a record 90,000 people apply for asylum last year, one of the highest levels per capita in Europe.
The far-right Freedom Party (FPÖ), in common with similar parties across Europe, has stoked concerns about the influx to boost its support.
Polls put the FPÖ's Norbert Hofer neck-and-neck with independent ecologist Alexander Van der Bellen to be elected to the largely but not entirely ceremonial post of president on December 4.
A victory for Hofer would make him Europe's first elected far-right head of state since 1945.