Tunisia has been the largest country of origin for foreign fighters joining the Islamic State group.
The German leader plans to press Youssef Chahed to speed up the repatriations of Tunisians, with the issue taking on greater urgency since the deadly assault on a Berlin Christmas market in December.
The jihadist attack which claimed 12 lives has been blamed on Anis Amri, a Tunisian whose asylum application had been rejected half a year earlier, but 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 has been under pressure to reduce the number of asylum seekers in Germany, after the country took in over a million migrants and refugees since 2015.
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 has 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.
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 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.
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.