Merkel plans to press Tunisia's Prime Minister Youssef Chahed to speed up the return of rejected asylum seekers when he visits Berlin Tuesday.
The issue has become more urgent for Germany since the deadly jihadist attack on a Berlin Christmas market last December, blamed on Anis Amri, a Tunisian who should have been sent back months before.
After the attack which claimed 12 lives, it emerged that Amri's asylum application had been rejected half a year earlier, but that he could not be expelled because of Tunisian bureaucratic delays.
Chahed however threw out any criticism.
"One thing that I must say very clearly: the Tunisian authorities have not made any mistakes," Chahed told Germany's biggest selling daily Bild.
"Anis Amri was no terrorist when he left Tunisia in 2011, there were no signs that he had been radicalised.
"With regards to the identity documents, here too, the Tunisian authorities acted correctly. We are always standing in close contact with Germany," he said.
Chahed said "cooperation with Germany works very well now" but threw the ball back in Berlin's court.
"We need from the German side clear evidence that we are really dealing with Tunisians," he said, estimating the number of Tunisian citizens concerned by possible expulsions from Germany at around 1,000.
"Illegal immigrants who use false identity documents make it difficult and delay the process."
Merkel plans to discuss with Chahed how to "work more quickly on this, especially in cases involving dangerous militants", she said in her weekly podcast message, adding that Tunis had signalled "a very positive" stance on the issue.
Germany has taken in over one million migrants and refugees since 2015, an influx that has heaped pressure on Merkel as she faces the rise of the anti-immigration AfD party ahead of September elections.
While most refugees from war-torn Syria have qualified for temporary safe haven, applicants from Tunisia as well as Algeria and Morocco generally have not, because their countries are considered stable.
Last year the success rates for asylum requests was 3.5 percent for Moroccans, 2.7 percent for Algerians and just 0.8 percent for Tunisians.
Merkel stressed that she wants Germany to list the three as "safe countries of origin", raising the bar for asylum requests further - but the proposal has been held up in the upper house of parliament in Berlin over human rights concerns.
Amnesty International this week alleged that a rise in "brutal tactics" by Tunisian security forces, including torture and arbitrary arrests, are threatening pro-democracy reforms in the country.
Interior Minister Thomas de Maiziere last year visited all three Maghreb countries to urge better cooperation on repatriations.
The question had already became a hot-button issue after New Year's Eve 2015-16, when mobs of North African men sexually assaulted and robbed hundreds of women in the western city of Cologne, sparking public outrage.
Germany, the top EU destination for refugees in recent years, worries that with the advent of spring, the number of migrants making the dangerous Mediterranean crossing will rise again.
Many are travelling via chaotic Libya, which has lacked a functioning national government since the 2011 overthrow of Moamer Kadhafi.
But Berlin also hopes other regional countries can help deter migrants from heading for the EU.
Merkel voiced support for a proposal for Tunisia to set up "holding facilities" for refugees rescued from the Mediterranean - an idea first proposed by Germany's centre-left Social Democrats.
She said that in her meeting with Chahed, they need "to calmly discuss, with mutual respect, what possibilities exist".
The German leader stressed that both countries could cooperate on security, a top issue for Tunisia with its important tourism sector.
Since the 2011 Tunisian revolution that sparked the Arab Spring, jihadist attacks have killed some 20 civilians, 59 foreign tourists and over 100 soldiers and police.
Tunisia has also been the largest country of origin for foreign fighters joining the Islamic State group, with over 5,500 of its nationals having flocked to the extremists' self-declared caliphate.
Nonetheless, Merkel called Tunisia a democratic beacon of "hope" and raised the prospect of development aid, including job training projects to reduce high youth unemployment.
The repatriation issue is sensitive for Tunisia, where many families rely on remittances sent back from relatives in Europe, and where mass protests were held last year against any plans to send home dangerous Tunisian jihadis.