The German leader has been battling to get Tunis to take back its citizens, 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.
But ahead of the meeting in Berlin, Tunisian Prime Minister Youssef Chahed threw out any criticism.
"Anis Amri was no terrorist when he left Tunisia in 2011, there were no signs that he had been radicalised.
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"With regards to the identity documents, here too, the Tunisian authorities acted correctly," 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 his fellow citizens concerned by possible expulsions from Germany at around 1,000.
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 per cent for Moroccans, 2.7 per cent for Algerians and just 0.8 per cent for Tunisians.
In a press conference following talks with Chahed, Merkel noted that only 116 Tunisians were repatriated last year.