Jan Hecker worked on the controversial refugee policy from October 2015, after Mrs Merkel announced Germany would take more than one million migrants.
The former federal judge led Germany’s migration treaties with African nations and accompanied Mrs Merkel on foreign trips focused on immigration.
Mr Hecker has been brought on to the chancellor’s team ahead of further tough coalition talks this week and next, during which it is expected immigration will be a key issue.
However his involvement is likely to provoke some awkward lines of questioning for Angela Merkel.
In a resounding rejection of her refugee policy, the CDU endured a battering by the far-right Alternative for Germany (AfD) in the September election and earned its worst result since 1949.
However despite U-turning on her open-door position she faces accusations of failing to learn her lesson after keeping the architect of the failed initiative so close.
It comes as members of Mrs Merkel’s CDU have attempted to distance themselves from the chancellor in order to avoid electoral oblivion.
Lower Saxony, in north-west Germany, was seen as a likely win for the CDU in Sunday’s local elections. The challenger from Mrs Merkel’s party, Bernd Althusmann, appeared set to replace the Socialist regional president Stephan Weil.
However Mr Althusmann is now on the defensive after realising the CDU’s popularity is in decline.
He said: “We would have liked to have more wind behind us.
“The refugee policy was misjudged. We have to make sure our values still align with the feelings of the population.”
Yesterday Mrs Merkel backtracked on her open-door immigration policy in a deal with the CDU’s main coalition partner, its Bavarian sister party the csu.
In a deal with CSU leader Horst Seehofer, the Chancellor agreed to an upper immigration limit of 200,000 new arrivals per year, as well as strict new immigration criteria that would make it harder to settle in Germany.
However she was subjected to awkward questions about why the deal could not have been done sooner.
One reporter suggested Mrs Merkel had “failed” the German people by not dealing with the problem of immigration before the far-right anti-immigration party Alternative for Germany (AfD) had been elected to the national parliament.